Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-11 23:55:01 -0400 (Sat, 11 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 8/33HostnameOS / ArchCHECK
biodbHmdb 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-11 09:55:01 -0400 (Sat, 11 May 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_19
git_last_commit: a7f41b2
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  WARNINGS  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on palomino3


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: 1.10.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz
StartedAt: 2024-05-11 16:04:45 -0400 (Sat, 11 May 2024)
EndedAt: 2024-05-11 17:29:30 -0400 (Sat, 11 May 2024)
EllapsedTime: 5084.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-05-11 16:06:29.180][biodb::testContext]
biodb.INFO [2024-05-11 16:06:29.183][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:06:29.184][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-11 16:06:29.185][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:06:29.186][biodb::testContext]
biodb.INFO [2024-05-11 16:06:29.193][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:06:29.195][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-11 16:06:29.203][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:06:29.204][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-11 16:06:29.206][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-11 16:06:29.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.210][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-11 16:06:29.230][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-11 16:06:29.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.235][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-11 16:06:29.236][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-11 16:06:29.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.240][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-11 16:06:29.242][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-11 16:06:29.243][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-11 16:06:29.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.248][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-11 16:06:29.249][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-11 16:06:29.250][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-11 16:06:29.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.255][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-11 16:06:29.256][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-11 16:06:29.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.260][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-11 16:06:29.261][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-11 16:06:29.263][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-11 16:06:29.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.267][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-11 16:06:29.268][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-11 16:06:29.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.273][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-11 16:06:29.274][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-11 16:06:29.275][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-11 16:06:29.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.280][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:06:29.281][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-11 16:06:29.282][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-11 16:06:29.283][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-11 16:06:29.285][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-11 16:06:29.286][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-11 16:06:29.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.290][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-11 16:06:29.291][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-11 16:06:29.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.296][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-11 16:06:29.297][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-11 16:06:29.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.302][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-11 16:06:29.303][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-11 16:06:29.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.307][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-11 16:06:29.309][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:06:29.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.313][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-11 16:06:29.314][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-11 16:06:29.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.319][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:06:29.320][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-11 16:06:29.324][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-11 16:06:29.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.328][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-11 16:06:29.329][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-11 16:06:29.331][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-11 16:06:29.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.337][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-11 16:06:29.372][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.387][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-11 16:06:29.388][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.389][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:06:29.391][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.392][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.393][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.394][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.395][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:06:29.397][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:06:29.398][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.399][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-11 16:06:29.400][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:06:29.401][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.403][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.404][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:06:29.404][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:06:29.404][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:06:29.404][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:06:29.404][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:06:29.405][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:06:29.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.409][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:06:29.410][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.412][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.413][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.415][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:06:29.416][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:06:29.417][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.418][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.419][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-11 16:06:29.421][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.423][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:06:29.424][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.425][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:06:29.426][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.427][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.429][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.430][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.431][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:06:29.432][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:06:29.433][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.435][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-11 16:06:29.436][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:06:29.437][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.438][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.439][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:06:29.439][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:06:29.439][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:06:29.439][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:06:29.439][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:06:29.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:06:29.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:06:29.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.448][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.449][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:06:29.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:06:29.452][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.453][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.455][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-11 16:06:29.457][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.458][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-11 16:06:29.459][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.460][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:06:29.462][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.463][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.464][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.465][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.466][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:06:29.468][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:06:29.469][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.470][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-11 16:06:29.471][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:06:29.473][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.474][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.475][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.476][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:06:29.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.480][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:06:29.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.483][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.484][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.485][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:06:29.487][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:06:29.488][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.489][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.490][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-11 16:06:29.492][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.494][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:06:29.495][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.496][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:06:29.497][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.498][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.500][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.501][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.502][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:06:29.503][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:06:29.504][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.506][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-11 16:06:29.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:06:29.508][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.509][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.510][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.512][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:06:29.513][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.515][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:06:29.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.519][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.520][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.521][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:06:29.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:06:29.523][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.524][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:29.528][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:06:29.529][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.632][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-11 16:06:29.636][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-11 16:06:29.638][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-11 16:06:29.639][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-11 16:06:29.641][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-11 16:06:29.642][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:06:29.644][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-11 16:06:29.645][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-11 16:06:29.647][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:06:29.649][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:06:29.650][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:06:29.652][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-11 16:06:29.653][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-11 16:06:29.655][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-11 16:06:29.656][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-11 16:06:29.658][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:06:29.659][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-11 16:06:29.661][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-11 16:06:29.663][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-11 16:06:29.664][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-11 16:06:29.666][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-11 16:06:29.667][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-11 16:06:29.669][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-11 16:06:29.671][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-11 16:06:29.672][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-11 16:06:29.674][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-11 16:06:29.675][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-11 16:06:29.677][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-11 16:06:29.678][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-11 16:06:29.680][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-11 16:06:29.681][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-11 16:06:29.683][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-11 16:06:29.684][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-11 16:06:29.686][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-11 16:06:29.688][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-11 16:06:29.689][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-11 16:06:29.691][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-11 16:06:29.692][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-11 16:06:29.694][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-11 16:06:29.695][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-11 16:06:29.697][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-11 16:06:29.698][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-11 16:06:29.700][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-11 16:06:29.701][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-11 16:06:29.703][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-11 16:06:29.705][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-11 16:06:29.706][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-11 16:06:29.708][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-11 16:06:29.709][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-11 16:06:29.711][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-11 16:06:29.712][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-11 16:06:29.714][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-11 16:06:29.715][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-11 16:06:29.717][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-11 16:06:29.719][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-11 16:06:29.720][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-11 16:06:29.722][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-11 16:06:29.723][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-11 16:06:29.725][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-11 16:06:29.726][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-11 16:06:29.728][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-11 16:06:29.729][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-11 16:06:29.731][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-11 16:06:29.733][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-11 16:06:29.734][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-11 16:06:29.736][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-11 16:06:29.737][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-11 16:06:29.739][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-11 16:06:29.740][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-11 16:06:29.742][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-11 16:06:29.744][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-11 16:06:29.745][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-11 16:06:29.747][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-11 16:06:29.748][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-11 16:06:29.750][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-11 16:06:29.751][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-11 16:06:29.753][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-11 16:06:29.754][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-11 16:06:29.756][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-11 16:06:29.758][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-11 16:06:29.759][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-11 16:06:29.761][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-11 16:06:29.762][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-11 16:06:29.803][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-11 16:06:29.805][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:06:29.809][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:06:29.810][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.812][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.948][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:06:29.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:06:29.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:29.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:29.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:29.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:29.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:29.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:06:29.959][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-05-11 16:06:29.968][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-05-11 16:06:29.970][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.971][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.972][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.974][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:06:29.975][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.976][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-05-11 16:06:29.977][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.978][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.980][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-11 16:06:29.981][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:06:29.982][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:29.983][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-05-11 16:06:29.984][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-05-11 16:06:29.986][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-05-11 16:06:29.987][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-11 16:06:29.988][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:06:29.988][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-05-11 16:06:29.988][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-05-11 16:06:29.989][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-11 16:06:29.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.993][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:06:29.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:06:29.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:06:29.996][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:06:29.998][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-05-11 16:06:29.998][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-05-11 16:06:29.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:06:30.000][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:06:30.001][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-11 16:06:30.002][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:06:30.034][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-05-11 16:06:30.036][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:06:30.038][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:06:30.040][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:06:30.041][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:06:30.063][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-05-11 16:06:30.064][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-05-11 16:06:30.068][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-05-11 16:06:30.072][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-05-11 16:06:30.075][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:06:30.077][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:06:30.078][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-05-11 16:06:30.079][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-05-11 16:06:30.089][biodb::testThat]
biodb.INFO [2024-05-11 16:06:30.090][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-11 16:06:30.092][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:06:30.093][biodb::testThat]
biodb.TRACE[2024-05-11 16:06:30.098][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-05-11 16:06:30.100][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-05-11 16:06:30.104][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-05-11 16:06:30.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:06:30.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:06:30.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:06:30.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:06:30.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:06:30.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:06:30.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:06:30.142][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.144][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.146][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.163][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.164][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.166][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.189][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.194][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.196][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.198][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.200][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.205][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.206][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.208][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.210][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.216][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.218][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.220][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.227][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.228][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.230][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.248][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.249][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.252][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.258][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.260][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.262][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.264][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.269][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.270][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.272][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.274][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.279][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.280][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.283][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.284][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.290][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:30.291][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:30.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.293][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:30.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:30.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.300][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:30.301][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:30.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.303][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:30.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:30.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.310][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.312][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.314][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.321][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.322][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.324][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.331][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.332][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.334][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.341][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:30.342][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:30.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.345][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.346][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:30.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:30.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.351][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:30.352][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:30.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.355][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.356][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:30.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:30.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.361][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-05-11 16:06:30.363][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:30.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.365][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.367][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-05-11 16:06:30.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:30.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.419][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.424][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.429][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:30.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.434][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.440][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.448][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:30.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:30.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:30.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.488][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.493][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:30.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.498][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.503][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.508][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:30.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.513][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:30.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:30.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.518][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:30.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:30.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.523][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:30.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:30.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.527][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:30.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:30.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.532][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:30.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:30.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.537][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:30.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:30.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.542][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:30.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:30.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:30.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:30.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.552][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:30.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:30.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:30.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:30.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:30.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:30.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:30.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:30.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.586][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.591][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.601][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:30.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.616][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:30.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.635][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.640][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.645][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:30.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.650][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.655][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.660][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.665][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:30.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.670][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:30.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:30.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.674][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:30.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:30.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.679][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-05-11 16:06:30.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.684][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.694][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.702][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-05-11 16:06:30.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:30.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:30.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:30.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.763][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.767][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.777][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:06:30.821][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-05-11 16:06:30.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:06:30.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:06:30.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.829][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:06:30.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:06:30.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.834][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:06:30.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:06:30.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.839][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:06:30.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:06:30.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.883][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.926][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.931][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.936][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 16:06:30.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.969][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.971][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.973][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:30.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:30.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:30.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:30.995][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:30.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.003][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.008][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.013][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.014][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.017][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.018][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.048][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.049][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.051][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.067][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.072][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.079][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.086][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.088][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.090][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.091][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.121][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.122][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.125][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.141][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.146][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.151][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.156][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.157][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.159][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.161][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.176][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:31.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:31.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:31.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:31.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:31.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:31.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.196][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:31.197][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:31.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.199][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:31.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:31.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.217][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:31.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:31.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.222][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:31.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:31.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.227][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:31.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:31.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.232][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:31.233][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:31.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.236][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.237][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:31.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:31.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:31.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:31.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.257][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:31.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:31.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.262][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:31.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:31.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.267][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:31.268][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:31.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.270][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:31.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:31.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.286][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.292][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.297][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.301][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.303][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.305][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.306][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.336][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.337][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.339][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.355][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.360][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.370][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.375][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.377][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.379][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.380][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.395][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.400][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.405][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.410][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.411][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.413][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.429][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.434][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.439][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.444][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.445][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.447][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.464][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:31.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:31.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.468][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:31.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:31.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.473][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:31.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:31.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.478][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:31.480][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:31.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.482][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.483][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:31.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:31.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:31.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:31.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:31.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:31.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:31.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:31.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.513][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:31.514][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:31.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.516][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:31.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:31.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.542][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.547][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.553][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.556][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.572][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.577][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.581][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.586][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.588][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.590][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.591][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.606][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:06:31.607][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:06:31.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.610][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.617][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.618][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-11 16:06:31.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.621][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.628][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.629][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:06:31.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.631][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.638][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.640][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-11 16:06:31.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.642][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.649][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.651][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-11 16:06:31.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.653][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.660][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.661][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-11 16:06:31.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.664][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.671][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.672][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-11 16:06:31.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.674][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.681][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.683][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-11 16:06:31.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.685][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.692][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-11 16:06:31.693][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 16:06:31.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.696][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.703][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:06:31.704][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:06:31.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.706][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.713][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:06:31.714][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:06:31.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.717][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.724][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.725][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:06:31.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.727][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.734][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.736][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-11 16:06:31.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.738][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.745][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.746][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-11 16:06:31.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.749][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.761][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:06:31.762][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:06:31.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.765][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.772][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.773][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-11 16:06:31.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.775][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.782][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.784][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 16:06:31.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.786][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:06:31.793][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-11 16:06:31.794][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-11 16:06:31.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:06:31.796][ef$get] fields variable is a list.
biodb.INFO [2024-05-11 16:06:31.809][biodb::testThat]
biodb.INFO [2024-05-11 16:06:31.810][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-11 16:06:31.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:06:31.812][biodb::testThat]
biodb.DEBUG[2024-05-11 16:06:31.826][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-05-11 16:06:31.832][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-05-11 16:06:31.838][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-05-11 16:06:31.840][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-05-11 16:06:31.842][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-05-11 16:06:31.843][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-05-11 16:06:31.845][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
==================================================
downloaded 909.7 MB

biodb.TRACE[2024-05-11 16:06:54.696][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\hmdb.metabolites175344b2d5dc6zip".
biodb.TRACE[2024-05-11 16:06:54.698][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-05-11 16:06:54.713][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-11 16:06:54.715][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-05-11 16:06:54.717][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-05-11 16:06:54.720][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker175342e5273damarker".
biodb.TRACE[2024-05-11 16:06:54.721][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-05-11 16:06:54.727][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-11 16:06:54.729][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-05-11 16:06:54.730][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-05-11 16:06:54.732][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-05-11 16:06:54.734][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-05-11 16:06:54.735][private$doExtractDownload] Unzipping C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp...
biodb.DEBUG[2024-05-11 16:07:29.102][private$findXmlDatabaseFile] Found files [1]: "hmdb_metabolites.xml" into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-05-11 16:07:29.103][private$findXmlDatabaseFile] Found XML file C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml in ZIP file.
biodb.DEBUG[2024-05-11 16:07:29.105][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-05-11 16:07:29.107][private$doExtractDownload] Extract entries from XML file "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml", into "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp".
biodb.TRACE[2024-05-11 16:24:48.647][self$addFilesToCache] Moving files to cache [217920]: "C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000001.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000002.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000005.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000008.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000010.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000011.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000012.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000014.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000015.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000016.xml, ...".
biodb.TRACE[2024-05-11 16:24:49.631][private$doAddFilesToCache] Destination files are [217920]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000005.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000008.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000010.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000011.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000012.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000014.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000015.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000016.xml, ...".
biodb.DEBUG[2024-05-11 17:29:04.973][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-11 17:29:04.981][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-05-11 17:29:05.080][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker175344d2a1530marker".
biodb.TRACE[2024-05-11 17:29:05.082][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-05-11 17:29:05.091][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-05-11 17:29:05.093][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-05-11 17:29:05.095][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-11 17:29:05.097][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-11 17:29:05.098][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-05-11 17:29:05.101][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-05-11 17:29:05.139][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-05-11 17:29:05.141][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-05-11 17:29:05.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 17:29:05.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 17:29:05.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 17:29:05.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 17:29:05.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 17:29:05.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 17:29:05.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 17:29:05.179][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 17:29:05.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 17:29:05.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:05.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:05.186][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 17:29:05.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-11 17:29:05.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:05.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:05.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 17:29:05.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 17:29:05.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:05.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:05.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 17:29:05.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 17:29:05.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:05.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:05.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 17:29:05.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 17:29:05.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:05.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:05.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 17:29:05.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 17:29:05.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:05.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:05.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 17:29:05.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 17:29:05.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:05.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:05.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 17:29:05.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 17:29:05.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:05.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 17:29:05.230][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-05-11 17:29:05.231][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-11 17:29:05.348][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.350][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-11 17:29:05.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 17:29:05.354][biodb::testThat]
biodb.TRACE[2024-05-11 17:29:05.360][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 17:29:05.362][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 17:29:05.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:05.364][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-11 17:29:05.371][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.INFO [2024-05-11 17:29:05.796][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.797][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-11 17:29:05.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 17:29:05.800][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.853][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.854][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-11 17:29:05.856][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 17:29:05.857][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.920][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.922][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-11 17:29:05.923][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 17:29:05.924][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.937][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.938][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-11 17:29:05.940][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 17:29:05.941][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.953][biodb::testThat]
biodb.INFO [2024-05-11 17:29:05.954][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-11 17:29:05.956][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 17:29:05.957][biodb::testThat]
biodb.DEBUG[2024-05-11 17:29:05.962][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-05-11 17:29:06.539][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-05-11 17:29:07.709][biodb::testThat]
biodb.INFO [2024-05-11 17:29:07.711][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-11 17:29:07.712][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 17:29:07.713][biodb::testThat]
biodb.DEBUG[2024-05-11 17:29:07.922][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-05-11 17:29:08.099][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 17:29:08.101][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 17:29:08.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:08.104][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:08.106][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-11 17:29:08.108][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 17:29:08.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:08.111][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:08.113][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 17:29:08.115][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 17:29:08.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:08.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:08.120][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 17:29:08.121][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 17:29:08.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:08.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:08.126][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-11 17:29:08.128][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-11 17:29:08.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:08.131][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 17:29:08.133][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-11 17:29:08.135][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-11 17:29:08.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 17:29:08.138][ef$get] fields variable is a list.
biodb.INFO [2024-05-11 17:29:08.140][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-11 17:29:08.142][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-05-11 17:29:08.144][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-05-11 17:29:08.145][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-11 17:29:08.147][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 17:29:08.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 17:29:08.150][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 17:29:08.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 17:29:08.153][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 17:29:08.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 7 | WARN 199315 | SKIP 0 | PASS 115 ]

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

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

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

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

[ FAIL 7 | WARN 199315 | SKIP 0 | PASS 115 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbHmdb/DESCRIPTION' ... OK
* this is package 'biodbHmdb' version '1.10.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'biodbHmdb' can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'zip'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'HmdbMetabolitesConn' 'HmdbMetabolitesEntry' 'hmdbToSqlite'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
  ── Failure ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
  `e` inherits from `'NULL'` not `'character'`.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─testthat::expect_is(e, "BiodbEntry")
  
  [ FAIL 7 | WARN 199315 | SKIP 0 | PASS 115 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log'
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package 'biodbHmdb' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor 'EntryMaker::EntryMaker()':
EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbHmdb.dll tmp.def EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'biodbHmdb' 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)