Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-05-04 23:55:02 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
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 10/33 | Hostname | OS / Arch | CHECK | |||||||
Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | ERROR | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
To the developers/maintainers of the biodbLipidmaps 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. |
Package: biodbLipidmaps |
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 biodbLipidmaps_1.10.0.tar.gz |
StartedAt: 2024-05-04 16:05:49 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 16:06:37 -0400 (Sat, 04 May 2024) |
EllapsedTime: 48.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbLipidmaps.Rcheck |
Warnings: NA |
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-15 r86425 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(biodbLipidmaps) Warning message: In fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbLipidmaps") biodb.INFO [2024-05-04 16:06:30.974][biodb::testContext] biodb.INFO [2024-05-04 16:06:30.977][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:06:30.978][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-05-04 16:06:30.980][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:06:30.981][biodb::testContext] biodb.INFO [2024-05-04 16:06:30.989][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:06:30.992][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:06:31.001][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:06:31.003][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:06:31.004][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:06:31.005][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.010][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:06:31.042][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:06:31.043][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.047][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:06:31.048][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:06:31.049][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.053][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:06:31.054][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:06:31.055][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:06:31.057][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.060][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:06:31.061][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:06:31.062][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:06:31.063][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.067][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:06:31.068][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:06:31.069][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.073][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:06:31.074][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:06:31.075][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:06:31.077][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.080][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:06:31.081][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:06:31.083][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.086][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:06:31.087][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:06:31.089][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:06:31.090][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.093][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:06:31.094][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:06:31.096][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:06:31.097][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:06:31.098][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:06:31.099][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:06:31.100][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.104][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:06:31.105][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:06:31.106][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.110][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:06:31.111][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:06:31.112][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.116][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:06:31.117][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:06:31.119][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.122][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:06:31.123][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:06:31.124][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.128][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:06:31.129][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:06:31.130][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.134][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:06:31.135][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:06:31.139][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:06:31.140][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.143][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:06:31.144][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:06:31.146][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:06:31.147][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.152][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:06:31.180][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.194][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 16:06:31.196][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.197][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:31.198][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.200][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:06:31.201][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.202][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:31.203][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:06:31.205][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:31.206][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.207][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:06:31.208][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:31.209][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.211][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.212][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:06:31.212][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:06:31.212][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:06:31.212][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:06:31.212][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:06:31.213][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:06:31.214][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.216][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.217][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:31.218][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.219][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.220][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:31.222][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.229][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:31.230][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:31.231][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.232][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.234][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:06:31.235][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.238][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:06:31.239][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.240][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:31.241][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.243][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:06:31.244][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:31.246][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:06:31.248][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:31.249][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.250][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:06:31.251][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:31.252][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.253][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.255][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:06:31.255][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:06:31.255][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:06:31.255][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:06:31.255][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:06:31.256][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:06:31.257][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.260][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:31.261][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.263][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:31.264][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.265][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:31.266][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:31.268][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.269][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.270][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:06:31.272][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.273][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 16:06:31.275][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.276][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:31.277][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.278][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:06:31.280][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.281][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:31.282][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:06:31.283][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:31.284][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.286][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:06:31.287][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:31.288][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.290][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.291][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.292][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:06:31.293][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.296][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:31.297][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.299][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:31.300][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.302][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:31.303][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:31.304][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.305][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.306][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:06:31.309][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.310][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:06:31.311][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.312][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:31.313][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.315][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:06:31.316][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.317][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:31.318][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:06:31.320][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:31.321][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.322][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:06:31.323][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:31.325][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.326][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.327][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.328][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:06:31.329][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.332][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:31.333][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.334][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.335][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:31.336][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.338][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:31.339][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:31.340][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.341][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.345][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:06:31.346][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.348][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.354][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.360][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.365][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.371][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.377][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.382][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.388][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.394][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.399][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.405][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.410][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.416][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.422][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.427][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.433][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.438][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.444][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:06:31.454][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:06:31.456][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:06:31.458][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:06:31.459][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:06:31.461][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:06:31.462][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:06:31.464][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:06:31.466][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:06:31.467][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:06:31.469][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:06:31.470][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:06:31.472][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:06:31.473][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:06:31.475][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:06:31.477][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:06:31.478][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:06:31.480][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:06:31.481][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:06:31.483][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:06:31.485][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:06:31.487][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:06:31.488][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:06:31.490][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:06:31.491][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:06:31.493][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:06:31.495][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:06:31.496][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:06:31.498][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:06:31.499][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:06:31.501][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:06:31.503][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:06:31.504][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:06:31.506][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:06:31.507][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:06:31.509][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:06:31.510][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:06:31.512][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:06:31.514][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:06:31.515][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:06:31.517][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:06:31.518][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:06:31.521][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:06:31.523][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:06:31.525][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:06:31.527][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:06:31.529][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:06:31.531][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:06:31.533][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:06:31.534][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:06:31.536][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:06:31.537][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:06:31.539][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:06:31.540][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:06:31.542][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:06:31.544][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:06:31.545][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:06:31.547][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:06:31.548][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:06:31.550][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:06:31.551][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:06:31.553][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:06:31.555][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:06:31.556][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:06:31.558][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:06:31.559][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:06:31.561][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:06:31.563][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:06:31.564][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:06:31.566][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:06:31.567][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:06:31.572][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:06:31.574][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:06:31.576][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:06:31.577][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:06:31.579][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:06:31.580][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:06:31.582][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:06:31.583][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:06:31.585][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:06:31.587][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:06:31.588][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:06:31.590][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:06:31.626][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:06:31.628][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:06:31.632][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:06:31.633][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.635][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.641][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.648][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.656][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.664][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.671][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.679][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.693][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.700][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.708][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.715][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.723][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.731][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.739][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.746][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.754][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.761][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.769][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:31.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:31.779][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/biodbLipidmaps/definitions.yml". biodb.DEBUG[2024-05-04 16:06:31.788][self$getDbsInfo()$define] Define connector lipidmaps.structure. biodb.DEBUG[2024-05-04 16:06:31.790][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.791][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-04 16:06:31.792][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.794][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:31.795][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.796][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:06:31.797][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.798][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:31.800][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:06:31.801][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:31.802][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.803][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure". biodb.DEBUG[2024-05-04 16:06:31.804][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:31.806][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID". biodb.DEBUG[2024-05-04 16:06:31.806][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID". biodb.DEBUG[2024-05-04 16:06:31.806][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID". biodb.DEBUG[2024-05-04 16:06:31.806][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID". biodb.DEBUG[2024-05-04 16:06:31.806][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID". biodb.DEBUG[2024-05-04 16:06:31.806][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME". biodb.DEBUG[2024-05-04 16:06:31.806][self$setPropertyValue] Setting property "parsing.expr" to "MASS". biodb.DEBUG[2024-05-04 16:06:31.806][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA". biodb.DEBUG[2024-05-04 16:06:31.806][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME". biodb.DEBUG[2024-05-04 16:06:31.807][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:06:31.808][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:06:31.808][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:06:31.809][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:06:31.811][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.813][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:31.814][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:31.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:31.816][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:31.817][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-05-04 16:06:31.817][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/". biodb.DEBUG[2024-05-04 16:06:31.819][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:31.820][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:31.821][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:31.822][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:31.828][self$getEntryFields()$define] Define field lipidmaps.structure.id. biodb.DEBUG[2024-05-04 16:06:31.829][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:06:31.855][initialize] Initialize connector lipidmaps.structure. biodb.DEBUG[2024-05-04 16:06:31.856][initialize] Register connector lipidmaps.structure with the request scheduler biodb.DEBUG[2024-05-04 16:06:31.860][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure. biodb.DEBUG[2024-05-04 16:06:31.864][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure". biodb.DEBUG[2024-05-04 16:06:31.868][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-04 16:06:31.869][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-05-04 16:06:31.871][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org". biodb.DEBUG[2024-05-04 16:06:31.872][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure . biodb.INFO [2024-05-04 16:06:31.882][biodb::testThat] biodb.INFO [2024-05-04 16:06:31.883][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-04 16:06:31.884][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:31.885][biodb::testThat] biodb.TRACE[2024-05-04 16:06:31.893][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv". biodb.DEBUG[2024-05-04 16:06:31.895][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-05-04 16:06:31.899][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 16:06:31.914][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:06:31.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:31.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:31.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:31.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:31.935][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:31.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:06:31.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:31.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:31.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:31.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:31.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:31.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:31.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:31.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:31.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:31.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:31.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:31.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:31.971][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:31.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:31.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:31.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:31.976][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:31.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:31.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:31.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:31.981][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:31.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:31.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:31.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.007][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.013][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.018][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.023][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 16:06:32.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.028][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 16:06:32.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.033][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.053][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 16:06:32.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.058][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-04 16:06:32.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.110][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 16:06:32.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.129][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.167][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.182][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.187][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:06:32.231][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001. biodb.TRACE[2024-05-04 16:06:32.234][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:06:32.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:06:32.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.239][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:06:32.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:06:32.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.244][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:06:32.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:06:32.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.253][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:06:32.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:06:32.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.297][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.340][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.350][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.381][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.383][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.384][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.385][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.416][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.417][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.419][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.420][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.441][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.447][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.452][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.456][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.458][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.459][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.460][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.461][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.476][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.491][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.493][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.494][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.495][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.527][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.528][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.529][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.530][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.552][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.557][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.562][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.563][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.564][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.565][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.567][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.582][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.583][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.584][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.585][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.592][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.594][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.595][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.596][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.603][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.604][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.606][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.607][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.614][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.615][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.616][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.617][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.624][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.631][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.632][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.633][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.640][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.642][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.643][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.644][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.664][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000002-content.tsv". biodb.DEBUG[2024-05-04 16:06:32.695][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-05-04 16:06:32.697][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 16:06:32.699][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:06:32.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:32.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:32.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:32.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:32.711][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:06:32.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:32.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:32.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:32.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:32.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.736][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:32.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:32.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.741][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:32.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:32.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.746][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.751][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:32.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.756][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.761][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:32.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.766][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 16:06:32.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.771][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 16:06:32.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:32.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.785][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:32.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:32.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.800][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 16:06:32.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.805][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-04 16:06:32.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.815][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:32.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.820][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 16:06:32.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:32.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.825][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.841][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:06:32.875][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000002. biodb.TRACE[2024-05-04 16:06:32.893][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:06:32.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:06:32.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.898][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:06:32.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:06:32.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.903][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:06:32.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:06:32.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.908][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:06:32.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:06:32.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:32.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:32.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.972][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.976][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:32.981][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:32.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:32.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.020][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.021][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.022][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.023][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.054][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.055][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.057][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.058][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.059][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.074][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.079][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.084][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.089][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.090][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.091][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.092][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.108][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.123][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.128][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.130][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.131][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.132][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.133][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.163][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.164][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.165][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.166][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.197][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.198][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.199][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.201][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.202][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.217][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.222][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.227][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.232][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.233][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.234][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.235][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.236][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.251][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.252][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.254][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.255][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.262][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.263][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.264][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.265][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.272][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.273][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.275][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.276][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.283][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.284][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.285][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.286][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.293][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.294][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.296][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.297][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.308][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.310][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.311][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.312][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.319][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.320][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.321][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.323][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.332][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA08040013-content.tsv". biodb.DEBUG[2024-05-04 16:06:33.334][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-05-04 16:06:33.335][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 16:06:33.337][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:06:33.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.346][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.348][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.350][FUN] Functions in observer BiodbConfig: [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[2024-05-04 16:06:33.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.374][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.379][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.384][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.389][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.394][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.399][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.404][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.409][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.414][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 16:06:33.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.419][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-05-04 16:06:33.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.424][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.429][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.434][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.444][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 16:06:33.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.449][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-05-04 16:06:33.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.464][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-05-04 16:06:33.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.469][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.499][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.504][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.514][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:06:33.549][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA08040013. biodb.TRACE[2024-05-04 16:06:33.551][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:06:33.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:06:33.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.556][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:06:33.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:06:33.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.561][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:06:33.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:06:33.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.567][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:06:33.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:06:33.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.584][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.627][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.632][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.637][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:33.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.672][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.673][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.674][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.676][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.707][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.709][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.710][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.711][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.727][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.732][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.737][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.742][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.743][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.745][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.746][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.747][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.762][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.776][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.778][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.779][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.780][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.796][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.801][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.806][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.811][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.813][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.814][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.815][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.816][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.848][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.850][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.856][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.857][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.873][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.879][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.884][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.888][ef$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.890][ef$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.891][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.892][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.893][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:33.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.908][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.914][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.919][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.924][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.925][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.926][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.927][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.929][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.959][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.960][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.961][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.962][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.979][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.980][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.982][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.983][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.990][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.991][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.992][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.994][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.001][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.002][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.003][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.004][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.011][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:34.013][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:34.014][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.015][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.022][ef$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.024][ef$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.025][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.026][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.033][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.035][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.036][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.037][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.049][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.050][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.051][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.053][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.060][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.061][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.062][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.063][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.070][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.072][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.073][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.074][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:06:34.087][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.088][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-04 16:06:34.089][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:34.090][biodb::testThat] biodb.DEBUG[2024-05-04 16:06:34.093][private$loadEntries] Creating entries from ids [3]: "LMFA00000001, LMFA00000002, LMFA08040013". biodb.DEBUG[2024-05-04 16:06:34.100][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 3 id(s)... biodb.TRACE[2024-05-04 16:06:34.106][cch$loadFileContent] Trying to load 3 files from cache: [3]: "LMFA00000001, LMFA00000002, LMFA08040013". biodb.TRACE[2024-05-04 16:06:34.109][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE". biodb.TRACE[2024-05-04 16:06:34.118][loadFileContents] Loaded 3 files from cache: [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv". biodb.DEBUG[2024-05-04 16:06:34.119][conn$getEntryContent] 3 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 16:06:34.121][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 3 content(s). biodb.DEBUG[2024-05-04 16:06:34.122][self$createEntryFromContent] Parsing 3 LIPID MAPS Structure entries. biodb.DEBUG[2024-05-04 16:06:34.124][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:06:34.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:34.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:34.134][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:34.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:34.136][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:34.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:06:34.139][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.144][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:06:34.154][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:06:34.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:34.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:34.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:34.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:34.165][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:34.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:06:34.169][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.174][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:06:34.183][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:06:34.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:34.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:34.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:34.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:34.195][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:34.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:06:34.198][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.203][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-05-04 16:06:34.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:06:34.293][self$createEntryFromContent] Accession numbers: NA, NA, NA. biodb.DEBUG[2024-05-04 16:06:34.294][self$createEntryFromContent] Found 3 entry/ies without an accession number. Set it/them to NULL. biodb.INFO [2024-05-04 16:06:34.315][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.317][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-04 16:06:34.318][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:34.319][biodb::testThat] biodb.TRACE[2024-05-04 16:06:34.323][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.324][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.325][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.326][ef$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:06:34.328][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name". biodb.INFO [2024-05-04 16:06:34.510][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.512][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-04 16:06:34.513][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:34.514][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.574][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.576][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-04 16:06:34.577][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:34.578][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.630][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.631][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-04 16:06:34.637][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:34.639][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.651][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.652][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-04 16:06:34.653][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:34.655][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.666][biodb::testThat] biodb.INFO [2024-05-04 16:06:34.667][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-04 16:06:34.668][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:34.669][biodb::testThat] biodb.DEBUG[2024-05-04 16:06:34.674][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001". biodb.DEBUG[2024-05-04 16:06:35.425][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001. biodb.INFO [2024-05-04 16:06:36.203][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.205][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-04 16:06:36.206][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:36.207][biodb::testThat] biodb.TRACE[2024-05-04 16:06:36.262][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:36.264][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:36.265][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:36.266][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:36.267][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:36.269][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:36.270][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:36.271][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:06:36.274][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.275][biodb::testThat] Running test function test.searchCompound (" We can search for a compound "). biodb.INFO [2024-05-04 16:06:36.276][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:36.277][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.515][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.517][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. "). biodb.INFO [2024-05-04 16:06:36.519][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:36.520][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.551][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.553][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() "). biodb.INFO [2024-05-04 16:06:36.555][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:36.557][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.587][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.588][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() "). biodb.INFO [2024-05-04 16:06:36.590][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:36.591][biodb::testThat] biodb.TRACE[2024-05-04 16:06:36.623][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:36.626][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:36.628][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:36.630][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:36.631][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:36.634][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:36.635][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:36.637][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:06:36.640][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.642][biodb::testThat] Running test function test.annotateMzValues_real_values (" annotateMzValues() works correctly with real values. "). biodb.INFO [2024-05-04 16:06:36.643][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:36.645][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.676][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.678][biodb::testThat] Running test function test_annotateMzValues_additional_fields (" Additional fields are accepted in annotateMzValues() "). biodb.INFO [2024-05-04 16:06:36.680][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:36.681][biodb::testThat] biodb.INFO [2024-05-04 16:06:36.715][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:06:36.717][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler biodb.INFO [2024-05-04 16:06:36.720][self$deleteConn] Connector "lipidmaps.structure" deleted. biodb.DEBUG[2024-05-04 16:06:36.722][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:06:36.723][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:36.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:36.726][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:36.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:36.729][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:36.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 14 | WARN 0 | SKIP 0 | PASS 150 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_long_100_generic.R:37:1'): 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 = `<LpdmpsSC>`, 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:37:1'): 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 = `<LpdmpsSC>`, opt = `<named list>`) 3. └─testthat::expect_true(!is.null(entry)) ── Error ('test_long_100_generic.R:37:1'): 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 = `<LpdmpsSC>`, opt = `<named list>`) ── Failure ('test_long_100_generic.R:37:1'): 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 = `<LpdmpsSC>`, opt = `<named list>`) 3. └─testthat::expect_true(!is.null(entry)) ── Error ('test_long_100_generic.R:37:1'): We can search for an entry by name. ── Error in `entry$getFieldValue("name")`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) ── Failure ('test_long_100_generic.R:37:1'): We can load an entry from the database. ── any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE `actual`: TRUE `expected`: FALSE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─opt$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:37:1'): 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 = `<LpdmpsSC>`, opt = `<named list>`) 3. └─testthat::expect_is(e, "BiodbEntry") ── Failure ('test_long_100_generic.R:37:1'): We can search for a compound ────── !is.null(entry) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`) 3. └─testthat::expect_true(!is.null(entry)) ── Error ('test_long_100_generic.R:37:1'): We can search for a compound ──────── Error in `entry$getFieldValue("name")`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`) ── Error ('test_long_100_generic.R:37:1'): annotateMzValues() accepts a single vector. ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): ppm tolerance works in annotateMzValues() ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): Input data frame is not modified by annotateMzValues() ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): annotateMzValues() works correctly with real values. ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): Additional fields are accepted in annotateMzValues() ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) [ FAIL 14 | WARN 0 | SKIP 0 | PASS 150 ] Error: Test failures Execution halted
############################################################################## ############################################################################## ### ### 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 biodbLipidmaps_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck' * using R version 4.4.0 beta (2024-04-15 r86425 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 'biodbLipidmaps/DESCRIPTION' ... OK * this is package 'biodbLipidmaps' 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 'biodbLipidmaps' can be installed ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): Additional fields are accepted in annotateMzValues() ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) [ FAIL 14 | WARN 0 | SKIP 0 | PASS 150 ] Error: Test failures Execution halted * DONE Status: 1 ERROR See 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/00check.log' for details.
biodbLipidmaps.Rcheck/00install.out
* installing *source* package 'biodbLipidmaps' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)