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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --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 16:01:55 -0400 (Sat, 05 Apr 2025)
EndedAt: 2025-04-05 16:03:15 -0400 (Sat, 05 Apr 2025)
EllapsedTime: 80.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 2

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu

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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 16:02:56.086][biodb::testContext]
biodb.INFO [2025-04-05 16:02:56.088][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-05 16:02:56.088][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-04-05 16:02:56.089][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-05 16:02:56.090][biodb::testContext]
biodb.INFO [2025-04-05 16:02:56.096][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-04-05 16:02:56.098][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-05 16:02:56.104][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:02:56.105][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-05 16:02:56.106][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-05 16:02:56.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.110][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-05 16:02:56.126][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-05 16:02:56.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.129][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.130][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-05 16:02:56.131][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-05 16:02:56.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.134][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-05 16:02:56.135][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-05 16:02:56.136][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-05 16:02:56.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.138][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.139][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-05 16:02:56.140][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-05 16:02:56.141][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-05 16:02:56.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.145][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-05 16:02:56.146][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-05 16:02:56.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.148][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.149][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-05 16:02:56.150][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-05 16:02:56.151][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-05 16:02:56.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.154][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-05 16:02:56.155][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-05 16:02:56.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.158][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.159][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-05 16:02:56.160][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-05 16:02:56.160][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-05 16:02:56.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.164][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-05 16:02:56.165][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-05 16:02:56.166][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-05 16:02:56.167][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-05 16:02:56.168][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-05 16:02:56.169][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-05 16:02:56.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.171][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.172][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-05 16:02:56.173][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-05 16:02:56.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.176][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-05 16:02:56.177][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-05 16:02:56.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.180][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.181][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-05 16:02:56.182][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-05 16:02:56.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.185][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-05 16:02:56.186][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-05 16:02:56.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.188][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.189][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-05 16:02:56.190][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-05 16:02:56.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.194][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-05 16:02:56.195][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-05 16:02:56.199][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-05 16:02:56.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.203][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-05 16:02:56.204][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-05 16:02:56.205][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-05 16:02:56.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.210][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-05 16:02:56.241][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.260][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-05 16:02:56.261][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.262][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:02:56.263][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.264][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.265][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.266][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.267][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-05 16:02:56.268][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:02:56.269][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.269][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-05 16:02:56.270][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:02:56.271][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.272][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.273][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:02:56.273][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-05 16:02:56.273][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-05 16:02:56.273][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-05 16:02:56.273][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-05 16:02:56.274][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:02:56.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.277][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:02:56.278][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.279][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.280][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.281][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:02:56.282][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:02:56.283][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.284][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.285][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-05 16:02:56.287][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.288][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-05 16:02:56.288][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.289][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:02:56.290][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.291][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.292][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.293][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.294][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-05 16:02:56.295][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:02:56.296][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.297][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-05 16:02:56.298][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:02:56.299][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.300][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.301][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:02:56.301][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-05 16:02:56.301][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-05 16:02:56.301][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-05 16:02:56.301][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-05 16:02:56.302][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:02:56.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.304][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:02:56.305][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.307][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.308][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.309][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:02:56.310][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:02:56.310][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.311][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.312][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-05 16:02:56.314][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.315][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-05 16:02:56.316][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.317][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:02:56.318][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.319][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.320][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.321][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.322][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-05 16:02:56.322][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:02:56.323][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.324][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-05 16:02:56.325][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:02:56.326][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.327][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.328][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.329][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:02:56.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.332][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:02:56.333][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.333][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.334][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.335][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.336][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:02:56.337][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:02:56.338][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.339][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.340][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-05 16:02:56.341][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.342][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-05 16:02:56.343][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.344][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:02:56.345][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.346][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.347][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.348][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.349][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-05 16:02:56.350][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:02:56.351][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.352][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-05 16:02:56.353][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:02:56.354][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.355][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.356][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.356][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:02:56.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.358][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.359][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:02:56.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.363][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.364][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:02:56.364][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:02:56.365][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.366][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.370][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:02:56.371][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.371][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.374][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 16:02:56.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.376][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:02:56.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.382][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 16:02:56.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.384][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.387][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 16:02:56.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.391][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 16:02:56.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.392][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.395][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 16:02:56.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.397][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:02:56.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.403][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 16:02:56.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.405][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.408][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 16:02:56.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.409][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.412][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 16:02:56.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.417][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.420][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 16:02:56.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.424][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 16:02:56.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.425][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.428][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 16:02:56.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.429][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:02:56.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.436][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 16:02:56.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.438][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.440][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 16:02:56.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.442][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.444][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 16:02:56.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.446][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.447][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-05 16:02:56.451][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-05 16:02:56.453][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-05 16:02:56.454][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-05 16:02:56.455][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-05 16:02:56.457][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-05 16:02:56.458][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-05 16:02:56.459][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-05 16:02:56.461][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-05 16:02:56.462][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-05 16:02:56.463][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-05 16:02:56.465][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-05 16:02:56.466][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-05 16:02:56.467][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-05 16:02:56.468][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-05 16:02:56.470][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-05 16:02:56.471][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-05 16:02:56.472][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-05 16:02:56.474][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-05 16:02:56.475][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-05 16:02:56.476][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-05 16:02:56.478][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-05 16:02:56.479][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-05 16:02:56.480][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-05 16:02:56.482][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-05 16:02:56.483][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-05 16:02:56.484][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-05 16:02:56.485][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-05 16:02:56.487][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-05 16:02:56.488][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-05 16:02:56.489][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-05 16:02:56.491][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-05 16:02:56.492][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-05 16:02:56.493][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-05 16:02:56.495][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-05 16:02:56.496][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-05 16:02:56.497][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-05 16:02:56.498][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-05 16:02:56.500][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-05 16:02:56.501][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-05 16:02:56.502][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-05 16:02:56.504][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-05 16:02:56.505][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-05 16:02:56.506][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-05 16:02:56.508][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-05 16:02:56.514][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-05 16:02:56.517][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-05 16:02:56.518][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-05 16:02:56.520][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-05 16:02:56.521][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-05 16:02:56.523][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-05 16:02:56.524][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-05 16:02:56.526][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-05 16:02:56.527][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-05 16:02:56.529][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-05 16:02:56.530][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-05 16:02:56.532][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-05 16:02:56.533][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-05 16:02:56.534][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-05 16:02:56.536][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-05 16:02:56.537][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-05 16:02:56.539][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-05 16:02:56.540][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-05 16:02:56.542][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-05 16:02:56.543][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-05 16:02:56.545][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-05 16:02:56.547][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-05 16:02:56.548][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-05 16:02:56.549][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-05 16:02:56.551][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-05 16:02:56.552][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-05 16:02:56.554][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-05 16:02:56.555][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-05 16:02:56.557][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-05 16:02:56.558][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-05 16:02:56.560][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-05 16:02:56.561][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-05 16:02:56.562][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-05 16:02:56.564][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-05 16:02:56.565][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-05 16:02:56.567][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-05 16:02:56.568][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-05 16:02:56.570][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-05 16:02:56.577][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-05 16:02:56.579][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-04-05 16:02:56.582][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:02:56.583][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.584][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 16:02:56.585][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.586][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.595][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 16:02:56.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.597][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 16:02:56.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.615][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 16:02:56.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.621][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 16:02:56.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.623][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.627][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 16:02:56.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.629][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.634][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 16:02:56.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.636][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.640][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 16:02:56.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.642][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.647][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 16:02:56.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.649][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:02:56.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:02:56.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.666][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 16:02:56.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.673][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 16:02:56.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.674][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.679][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 16:02:56.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.685][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 16:02:56.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.687][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.691][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 16:02:56.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.693][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.698][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 16:02:56.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.700][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.704][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 16:02:56.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.706][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:02:56.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:02:56.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.713][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-05 16:02:56.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:02:56.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:02:56.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:02:56.720][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-04-05 16:02:56.729][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-04-05 16:02:56.731][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.732][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.733][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.734][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:02:56.735][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.736][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-04-05 16:02:56.737][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.738][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.739][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-05 16:02:56.740][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:02:56.741][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.742][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-04-05 16:02:56.743][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-04-05 16:02:56.744][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-04-05 16:02:56.745][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-05 16:02:56.746][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:02:56.746][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-04-05 16:02:56.746][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-04-05 16:02:56.747][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-05 16:02:56.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.749][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:02:56.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:02:56.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:02:56.752][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:02:56.753][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-04-05 16:02:56.753][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-04-05 16:02:56.754][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:02:56.755][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:02:56.756][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-05 16:02:56.757][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:02:56.762][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-04-05 16:02:56.763][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-05 16:02:56.765][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-05 16:02:56.766][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-05 16:02:56.768][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-05 16:02:56.789][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-04-05 16:02:56.790][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-04-05 16:02:56.820][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-04-05 16:02:56.823][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-04-05 16:02:56.827][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-05 16:02:56.828][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-05 16:02:56.829][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-04-05 16:02:56.830][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-04-05 16:02:56.838][biodb::testThat]
biodb.INFO [2025-04-05 16:02:56.839][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-05 16:02:56.840][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:02:56.841][biodb::testThat]
biodb.TRACE[2025-04-05 16:02:56.844][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-04-05 16:02:56.846][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-04-05 16:02:56.849][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-04-05 16:02:56.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-05 16:02:56.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:56.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:56.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:56.871][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 16:02:56.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:56.872][FUN] Functions in observer BiodbConfig: [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 16:02:56.883][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:56.884][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:56.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.885][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:56.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:56.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.902][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:56.903][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:56.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.905][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.929][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:56.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:56.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.933][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:56.934][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:56.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.936][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.937][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:56.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:56.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.941][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:56.942][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:56.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.943][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.945][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:56.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:56.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.949][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:56.950][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:56.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.951][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:56.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:56.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.956][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:56.958][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:56.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.959][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:56.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:56.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.964][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:56.965][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:56.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.967][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.969][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:56.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:56.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.972][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:56.973][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:56.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.975][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.977][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:56.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:56.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.980][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:56.988][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:56.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.990][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.992][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:56.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:56.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.995][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:56.996][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:56.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:56.998][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:56.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.003][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.004][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.006][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.007][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.011][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.012][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.014][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.019][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.020][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.022][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.027][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.028][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.029][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.034][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.035][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.037][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.042][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.043][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.045][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.046][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.050][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.051][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.053][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.054][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.058][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-04-05 16:02:57.059][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.060][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.062][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-04-05 16:02:57.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.107][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.111][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.115][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.123][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.126][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.130][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.157][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.161][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.164][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.168][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.172][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.176][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.180][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.183][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.191][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.194][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.198][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.236][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.239][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.243][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.272][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.276][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.284][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.287][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.291][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.295][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.299][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.302][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.306][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-05 16:02:57.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.317][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.321][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-05 16:02:57.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.348][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.360][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.363][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.371][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:57.397][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-04-05 16:02:57.403][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:02:57.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:02:57.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.406][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:02:57.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:02:57.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.410][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:02:57.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:02:57.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.414][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:02:57.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:02:57.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.445][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.477][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.480][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.484][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:57.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.505][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.506][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.508][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.519][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.522][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.526][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.530][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.531][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.533][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.534][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:57.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.558][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.559][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.561][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.572][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.576][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.579][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.583][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.584][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.586][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.587][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:57.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.608][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.609][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.611][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.621][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.625][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.629][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.633][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.634][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.635][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.636][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:57.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.650][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.657][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.658][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.660][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:57.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:57.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.671][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.678][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.682][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.685][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.686][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.688][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.689][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:57.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:57.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.699][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.703][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.706][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.710][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.711][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.713][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.714][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:57.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:57.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.724][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.727][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.731][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.735][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.736][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.738][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.739][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.760][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.761][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.762][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:57.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.773][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.777][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.781][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.784][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.785][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.787][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:57.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.798][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.802][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.805][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.813][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.814][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.815][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.816][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.830][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.834][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.837][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.838][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.840][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.841][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.851][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.855][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.858][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.862][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.863][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.865][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.866][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:57.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:57.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.887][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.888][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.889][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:57.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:57.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.912][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.913][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.914][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:57.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.925][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.929][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.932][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.936][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.937][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.939][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.940][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.953][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:57.954][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:57.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.956][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.960][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.961][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:57.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.963][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.966][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.967][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:57.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.969][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.973][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.974][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:57.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.976][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.979][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.980][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:57.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.982][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.986][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.987][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:57.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.989][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.992][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.993][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:57.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:57.995][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:57.999][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.000][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.002][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.006][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.007][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.008][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.012][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:58.013][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:58.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.015][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.019][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:58.020][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:58.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.021][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.025][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.026][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.028][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.032][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.033][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.034][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.038][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.039][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.041][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.045][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.046][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.048][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.051][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.052][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.054][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.058][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.059][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.061][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.064][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:58.065][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:58.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.067][ef$get] fields variable is a list.
biodb.INFO [2025-04-05 16:02:58.074][biodb::testThat]
biodb.INFO [2025-04-05 16:02:58.074][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-05 16:02:58.075][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:02:58.080][biodb::testThat]
biodb.DEBUG[2025-04-05 16:02:58.093][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-04-05 16:02:58.099][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-04-05 16:02:58.103][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.105][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-04-05 16:02:58.106][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-04-05 16:02:58.107][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-04-05 16:02:58.110][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-04-05 16:02:58.111][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-04-05 16:02:58.133][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-04-05 16:02:58.134][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-04-05 16:02:58.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-05 16:02:58.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:02:58.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:02:58.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:02:58.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:02:58.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:02:58.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-05 16:02:58.148][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.149][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.150][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.155][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.156][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.158][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.159][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.163][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.164][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.166][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.167][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.171][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.172][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.174][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.175][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.179][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.180][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.182][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.187][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.188][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.189][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.194][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.195][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.197][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.198][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.202][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.203][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.205][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.206][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.210][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.211][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.212][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.217][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.218][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.222][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.223][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.224][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.226][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.229][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:58.230][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:58.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.232][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.233][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:58.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:58.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.237][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:58.238][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:58.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.240][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:58.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:58.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.245][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.246][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.248][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.252][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.253][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.255][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.260][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.261][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.263][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.268][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.269][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.271][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.272][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.275][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:58.276][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:58.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.278][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:58.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:58.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.283][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-04-05 16:02:58.284][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.286][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.287][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-04-05 16:02:58.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.302][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.306][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.310][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-05 16:02:58.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.313][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.317][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.321][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:02:58.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-05 16:02:58.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-05 16:02:58.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.347][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.354][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.358][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-05 16:02:58.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.365][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.369][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-05 16:02:58.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.372][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.380][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-05 16:02:58.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.384][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.387][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.391][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.395][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:58.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:58.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.398][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:58.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:58.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.402][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:02:58.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:02:58.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:58.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:58.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:58.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:58.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:02:58.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:02:58.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.428][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.432][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.436][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-05 16:02:58.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-05 16:02:58.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.462][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.465][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-05 16:02:58.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.473][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.476][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.483][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.487][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:58.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:58.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.491][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:58.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:58.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.495][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-05 16:02:58.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-05 16:02:58.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.498][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-05 16:02:58.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.513][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-05 16:02:58.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:02:58.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.521][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.532][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.536][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:58.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:58.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.540][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:58.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:58.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.547][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:58.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-05 16:02:58.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:02:58.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:02:58.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.574][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-04-05 16:02:58.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-05 16:02:58.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-05 16:02:58.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-05 16:02:58.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-05 16:02:58.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-05 16:02:58.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-05 16:02:58.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-05 16:02:58.592][biodb::testThat]
biodb.INFO [2025-04-05 16:02:58.593][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-05 16:02:58.594][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:02:58.595][biodb::testThat]
biodb.TRACE[2025-04-05 16:02:58.597][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.598][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.600][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.601][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-04-05 16:02:58.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.641][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-04-05 16:02:58.642][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-04-05 16:02:58.643][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-04-05 16:02:58.644][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-04-05 16:02:58.646][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.647][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.648][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-04-05 16:02:58.650][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.651][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-04-05 16:02:58.652][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-04-05 16:02:58.653][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-04-05 16:02:58.654][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-04-05 16:02:58.655][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-04-05 16:02:58.656][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-04-05 16:02:58.657][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-04-05 16:02:58.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.673][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-04-05 16:02:58.674][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-04-05 16:02:58.675][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-04-05 16:02:58.685][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.686][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.687][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.688][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-04-05 16:02:58.698][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.702][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.706][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.711][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 16:02:58.764][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-04-05 16:02:58.765][private$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 16:02:58.766][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-04-05 16:02:58.779][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.780][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.781][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-04-05 16:02:58.782][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.783][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-04-05 16:02:58.797][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-04-05 16:02:58.798][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-04-05 16:02:58.799][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-04-05 16:02:58.800][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-04-05 16:02:58.801][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-04-05 16:02:58.802][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-04-05 16:02:58.804][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.807][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.811][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.815][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:02:58.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:02:58.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.819][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-04-05 16:02:58.820][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-04-05 16:02:58.820][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-04-05 16:02:58.830][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.831][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.833][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.834][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-04-05 16:02:58.843][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.847][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.851][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.860][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-04-05 16:02:58.861][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-04-05 16:02:58.862][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-04-05 16:02:58.863][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-04-05 16:02:58.865][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.866][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.867][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-04-05 16:02:58.869][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.869][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-04-05 16:02:58.871][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-04-05 16:02:58.872][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-04-05 16:02:58.873][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-04-05 16:02:58.873][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-04-05 16:02:58.874][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-04-05 16:02:58.875][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-04-05 16:02:58.877][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.881][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.884][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.888][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:02:58.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.892][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-04-05 16:02:58.893][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-04-05 16:02:58.894][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-04-05 16:02:58.906][biodb::testThat]
biodb.INFO [2025-04-05 16:02:58.906][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-05 16:02:58.907][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:02:58.908][biodb::testThat]
biodb.TRACE[2025-04-05 16:02:58.917][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.921][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.937][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-04-05 16:02:58.938][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-04-05 16:02:58.939][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-04-05 16:02:58.940][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.941][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.943][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-04-05 16:02:58.944][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-04-05 16:02:58.945][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-04-05 16:02:58.946][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-04-05 16:02:58.947][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-04-05 16:02:58.948][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-04-05 16:02:58.949][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-04-05 16:02:58.950][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-04-05 16:02:58.951][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-04-05 16:02:58.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:58.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:02:58.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:02:58.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:58.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:02:58.967][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-04-05 16:02:58.968][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-04-05 16:02:58.980][biodb::testThat]
biodb.INFO [2025-04-05 16:02:58.981][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-05 16:02:58.982][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:02:58.983][biodb::testThat]
biodb.TRACE[2025-04-05 16:02:59.004][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:02:59.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:02:59.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:59.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:59.008][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:02:59.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:02:59.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:59.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:59.012][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:02:59.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:02:59.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:59.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:59.016][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:02:59.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:02:59.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:59.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:59.060][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:02:59.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:02:59.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:59.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:59.065][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:02:59.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:02:59.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:59.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:59.069][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:02:59.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:02:59.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:59.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:02:59.073][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:02:59.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:02:59.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:02:59.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-05 16:02:59.082][biodb::testThat]
biodb.INFO [2025-04-05 16:02:59.083][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-05 16:02:59.084][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:02:59.085][biodb::testThat]
biodb.INFO [2025-04-05 16:02:59.092][biodb::testThat]
biodb.INFO [2025-04-05 16:02:59.093][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-05 16:02:59.094][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:02:59.095][biodb::testThat]
biodb.INFO [2025-04-05 16:02:59.102][biodb::testThat]
biodb.INFO [2025-04-05 16:02:59.103][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-05 16:02:59.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:02:59.105][biodb::testThat]
biodb.DEBUG[2025-04-05 16:02:59.108][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-04-05 16:03:12.540][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-04-05 16:03:12.602][biodb::testThat]
biodb.INFO [2025-04-05 16:03:12.604][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-05 16:03:12.607][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:03:12.609][biodb::testThat]
biodb.DEBUG[2025-04-05 16:03:14.121][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-04-05 16:03:14.162][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:03:14.174][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:03:14.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:03:14.176][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:03:14.177][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:03:14.178][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:03:14.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:03:14.180][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:03:14.181][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:03:14.182][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:03:14.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:03:14.184][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:03:14.186][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:03:14.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:03:14.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:03:14.189][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:03:14.190][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-05 16:03:14.191][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-05 16:03:14.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:03:14.193][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:03:14.194][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-05 16:03:14.195][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-05 16:03:14.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:03:14.197][ef$get] fields variable is a list.
biodb.INFO [2025-04-05 16:03:14.198][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-05 16:03:14.199][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-04-05 16:03:14.200][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-04-05 16:03:14.201][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-05 16:03:14.202][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:03:14.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:03:14.204][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:03:14.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:03:14.205][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:03:14.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 147 ]
> 
> proc.time()
   user  system elapsed 
  4.726   0.260  19.733

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --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 ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* 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 for sufficient/correct file permissions ... 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 ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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
  ‘/home/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++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so 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 -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)