| Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-07-13 23:55 -0400 (Sat, 13 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 8/33 | Hostname | OS / Arch | CHECK | |||||||
| biodbHmdb 1.10.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | ERROR | |||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | ERROR | ||||||||
|
To the developers/maintainers of the biodbHmdb package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbHmdb |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz |
| StartedAt: 2024-07-13 16:01:30 -0400 (Sat, 13 Jul 2024) |
| EndedAt: 2024-07-13 16:11:54 -0400 (Sat, 13 Jul 2024) |
| EllapsedTime: 623.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: NA |
biodbHmdb.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-07-13 16:03:14.051][biodb::testContext]
biodb.INFO [2024-07-13 16:03:14.055][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:03:14.056][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-13 16:03:14.057][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:03:14.058][biodb::testContext]
biodb.INFO [2024-07-13 16:03:14.065][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:03:14.067][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-13 16:03:14.075][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:03:14.077][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-13 16:03:14.078][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-13 16:03:14.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.083][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-13 16:03:14.107][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-13 16:03:14.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.112][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-13 16:03:14.113][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-13 16:03:14.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.118][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-13 16:03:14.119][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-13 16:03:14.121][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-13 16:03:14.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.125][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-13 16:03:14.126][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-13 16:03:14.128][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-13 16:03:14.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.132][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-13 16:03:14.133][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-13 16:03:14.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.137][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.DEBUG[2024-07-13 16:03:14.138][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-13 16:03:14.139][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-13 16:03:14.140][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-13 16:03:14.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.145][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-13 16:03:14.146][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-13 16:03:14.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.149][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[2024-07-13 16:03:14.150][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-13 16:03:14.152][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-13 16:03:14.153][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-13 16:03:14.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.158][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:03:14.159][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-13 16:03:14.160][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-13 16:03:14.161][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-13 16:03:14.162][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-13 16:03:14.164][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-13 16:03:14.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.167][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.DEBUG[2024-07-13 16:03:14.168][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-13 16:03:14.170][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-13 16:03:14.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.174][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-13 16:03:14.175][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-13 16:03:14.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.180][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-13 16:03:14.181][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-13 16:03:14.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.186][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-13 16:03:14.187][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:03:14.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.191][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-13 16:03:14.193][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-13 16:03:14.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.197][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:03:14.199][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-13 16:03:14.209][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-13 16:03:14.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.214][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-13 16:03:14.215][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-13 16:03:14.217][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-13 16:03:14.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.224][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-13 16:03:14.268][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.297][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-13 16:03:14.298][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.300][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:14.301][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.302][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.303][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.304][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.306][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:03:14.307][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:14.308][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.309][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-13 16:03:14.311][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:14.312][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.313][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.315][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:03:14.315][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:03:14.315][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:03:14.315][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:03:14.315][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:03:14.316][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:03:14.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.320][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:14.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.322][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.323][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.324][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.326][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:14.327][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:14.328][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.329][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.331][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-13 16:03:14.333][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.334][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:03:14.335][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.337][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:14.338][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.339][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.340][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.342][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.343][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:03:14.344][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:14.345][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.347][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-13 16:03:14.348][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:14.349][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.350][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.352][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:03:14.352][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:03:14.352][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:03:14.352][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:03:14.352][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:03:14.353][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:03:14.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:14.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.360][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.361][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.362][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:14.363][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:14.365][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.366][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.367][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-13 16:03:14.369][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.371][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-13 16:03:14.372][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:14.374][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.376][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.377][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.378][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.379][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:03:14.381][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:14.382][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.383][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-13 16:03:14.384][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:14.385][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.387][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.388][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.389][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:03:14.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.393][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:14.394][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.396][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.397][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.399][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:14.400][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:14.401][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.402][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.403][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-13 16:03:14.406][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.407][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:03:14.408][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.409][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:14.411][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.412][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.413][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.414][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.415][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:03:14.417][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:14.418][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.419][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-13 16:03:14.420][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:14.422][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.423][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.424][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.425][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:03:14.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.429][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:14.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.432][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.434][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.435][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:14.436][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:14.437][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.438][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.443][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:03:14.444][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.547][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-13 16:03:14.552][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-13 16:03:14.554][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-13 16:03:14.556][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-13 16:03:14.558][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-13 16:03:14.560][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:03:14.561][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-13 16:03:14.563][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-13 16:03:14.565][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:03:14.566][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:03:14.568][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:03:14.570][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-13 16:03:14.572][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-13 16:03:14.573][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-13 16:03:14.575][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-13 16:03:14.577][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:03:14.578][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-13 16:03:14.580][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-13 16:03:14.582][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-13 16:03:14.583][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-13 16:03:14.585][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-13 16:03:14.587][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-13 16:03:14.589][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-13 16:03:14.590][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-13 16:03:14.592][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-13 16:03:14.594][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-13 16:03:14.595][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-13 16:03:14.597][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-13 16:03:14.599][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-13 16:03:14.601][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-13 16:03:14.602][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-13 16:03:14.604][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-13 16:03:14.606][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-13 16:03:14.607][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-13 16:03:14.609][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-13 16:03:14.611][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-13 16:03:14.612][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-13 16:03:14.614][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-13 16:03:14.616][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-13 16:03:14.618][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-13 16:03:14.619][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-13 16:03:14.621][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-13 16:03:14.623][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-13 16:03:14.625][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-13 16:03:14.627][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-13 16:03:14.628][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-13 16:03:14.630][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-13 16:03:14.632][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-13 16:03:14.634][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-13 16:03:14.635][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-13 16:03:14.637][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-13 16:03:14.639][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-13 16:03:14.641][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-13 16:03:14.642][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-13 16:03:14.644][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-13 16:03:14.646][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-13 16:03:14.648][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-13 16:03:14.650][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-13 16:03:14.652][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-13 16:03:14.653][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-13 16:03:14.655][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-13 16:03:14.657][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-13 16:03:14.659][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-13 16:03:14.661][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-13 16:03:14.662][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-13 16:03:14.664][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-13 16:03:14.666][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-13 16:03:14.668][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-13 16:03:14.669][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-13 16:03:14.671][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-13 16:03:14.673][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-13 16:03:14.675][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-13 16:03:14.676][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-13 16:03:14.678][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-13 16:03:14.680][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-13 16:03:14.682][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-13 16:03:14.683][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-13 16:03:14.685][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-13 16:03:14.687][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-13 16:03:14.689][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-13 16:03:14.691][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-13 16:03:14.693][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-13 16:03:14.694][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-13 16:03:14.703][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-13 16:03:14.705][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:03:14.709][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:03:14.710][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.712][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.860][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:03:14.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:03:14.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:14.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:14.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:14.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:14.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:14.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:03:14.870][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-07-13 16:03:14.883][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-07-13 16:03:14.886][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.887][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.890][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:03:14.891][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.892][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-07-13 16:03:14.894][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.895][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.897][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-13 16:03:14.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:03:14.900][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.902][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-07-13 16:03:14.903][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-07-13 16:03:14.905][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-07-13 16:03:14.907][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-13 16:03:14.908][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:03:14.908][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-07-13 16:03:14.908][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-07-13 16:03:14.910][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-13 16:03:14.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.914][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:03:14.915][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:03:14.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:03:14.918][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:03:14.919][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-07-13 16:03:14.919][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-07-13 16:03:14.920][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:03:14.922][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:03:14.923][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-13 16:03:14.924][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:03:14.932][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-07-13 16:03:14.935][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:03:14.937][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:03:14.939][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:03:14.941][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:03:14.966][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-07-13 16:03:14.967][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-07-13 16:03:14.972][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-07-13 16:03:15.005][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-07-13 16:03:15.009][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:03:15.012][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:03:15.014][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-07-13 16:03:15.016][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-07-13 16:03:15.026][biodb::testThat]
biodb.INFO [2024-07-13 16:03:15.028][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-07-13 16:03:15.029][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:03:15.030][biodb::testThat]
biodb.TRACE[2024-07-13 16:03:15.034][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-07-13 16:03:15.037][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-07-13 16:03:15.041][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-07-13 16:03:15.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:03:15.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:03:15.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:03:15.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:03:15.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:03:15.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:03:15.073][FUN] Functions in observer BiodbConfig: [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[2024-07-13 16:03:15.085][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.087][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.089][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.113][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.114][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.116][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.152][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.158][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.159][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.161][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.163][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.168][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.169][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.171][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.172][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.173][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.180][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.182][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.189][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.190][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.193][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.199][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.201][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.203][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.204][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.210][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.211][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.213][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.215][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.220][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.221][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.224][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.232][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.237][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.239][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.241][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.243][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.247][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:15.249][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:15.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.251][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.253][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:15.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:15.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.258][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:15.259][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:15.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.262][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:15.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:15.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.268][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.270][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.272][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.279][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.280][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.282][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.289][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.290][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.293][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.299][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:15.301][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:15.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.303][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.304][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:15.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:15.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.309][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:15.311][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:15.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.313][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.315][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:15.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:15.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.320][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-07-13 16:03:15.321][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:15.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.323][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.325][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-07-13 16:03:15.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:15.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.391][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.397][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.402][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:15.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.407][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.412][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.420][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:15.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:15.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.460][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:15.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.469][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:15.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.484][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:15.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:15.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.489][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:15.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:15.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.494][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:15.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:15.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.499][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:15.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:15.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.504][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:15.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:15.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.509][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:15.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:15.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.513][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:15.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:15.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:15.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:15.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:15.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:15.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:15.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:15.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:15.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:15.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:15.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:15.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.558][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.563][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.568][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:15.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:15.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.606][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.611][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.616][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:15.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.621][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.626][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.631][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.636][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:15.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:15.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.640][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:15.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:15.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.645][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:15.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:15.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.650][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-07-13 16:03:15.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.660][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.670][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-07-13 16:03:15.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:15.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.713][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.718][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:15.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:15.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.723][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.728][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:03:15.772][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-07-13 16:03:15.775][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:03:15.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:03:15.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.780][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:03:15.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:03:15.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.789][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:03:15.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:03:15.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:03:15.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:03:15.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.838][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.880][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.885][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.890][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:03:15.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.924][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.925][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.928][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:15.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:15.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.947][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.952][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.957][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.962][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.963][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.965][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.967][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:15.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:15.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:15.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:15.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:16.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:16.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.005][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:16.006][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:16.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.009][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:16.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:16.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.025][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.030][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.035][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.040][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.041][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.043][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.044][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.074][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.075][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.077][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.094][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.103][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.109][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.118][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.119][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.122][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.123][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:16.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:16.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:16.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:16.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:16.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:16.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.156][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:16.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:16.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.159][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:16.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:16.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.176][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:16.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:16.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.181][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:16.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:16.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.186][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:16.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:16.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.191][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:16.192][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:16.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.195][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.200][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:16.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:16.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:16.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:16.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:16.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:16.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:16.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:16.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.230][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:16.232][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:16.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.234][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.235][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:16.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:16.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.251][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.256][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.261][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.266][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.267][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.269][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.271][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.302][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.303][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.305][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.321][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.326][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.331][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.336][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.338][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.340][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.341][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.356][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.361][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.366][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.371][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.373][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.375][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.376][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.396][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.401][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.406][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.411][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.413][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.415][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.416][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.431][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:16.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:16.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.436][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:16.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:16.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.441][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:16.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:16.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.446][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:16.448][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:16.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.450][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.451][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:16.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:16.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.467][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:16.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:16.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:16.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:16.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:16.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:16.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.483][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:16.484][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:16.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.487][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:16.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:16.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.519][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.521][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.523][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.524][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.539][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.545][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.550][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.555][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.556][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.558][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.559][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.574][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:03:16.576][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:03:16.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.578][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.584][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.590][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:03:16.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.592][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.599][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.600][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:03:16.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.602][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.609][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.611][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:03:16.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.613][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.619][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:16.621][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:03:16.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.623][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.629][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.630][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:03:16.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.633][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.640][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.641][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:03:16.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.644][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.650][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.652][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:03:16.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.654][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.661][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:03:16.662][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:03:16.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.664][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.670][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:03:16.672][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:03:16.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.674][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.680][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:03:16.682][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:03:16.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.684][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.690][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.692][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:03:16.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.694][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.700][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.702][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:03:16.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.704][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.710][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.711][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:03:16.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.714][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.720][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:03:16.722][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:03:16.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.724][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.730][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.732][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:03:16.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.734][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.740][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:16.742][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:03:16.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.744][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:03:16.750][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:03:16.752][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:03:16.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:03:16.754][ef$get] fields variable is a list.
biodb.INFO [2024-07-13 16:03:16.765][biodb::testThat]
biodb.INFO [2024-07-13 16:03:16.766][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-13 16:03:16.767][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:03:16.768][biodb::testThat]
biodb.DEBUG[2024-07-13 16:03:16.788][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-07-13 16:03:16.800][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-07-13 16:03:16.805][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-07-13 16:03:16.806][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-07-13 16:03:16.808][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-07-13 16:03:16.809][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-07-13 16:03:16.812][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
=================
downloaded 315.5 MB
biodb.INFO [2024-07-13 16:06:09.032][biodb::testThat]
biodb.INFO [2024-07-13 16:06:09.033][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-13 16:06:09.035][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:09.036][biodb::testThat]
biodb.TRACE[2024-07-13 16:06:09.040][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:06:09.041][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:06:09.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:06:09.044][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:06:09.045][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2024-07-13 16:06:09.076][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-07-13 16:06:09.147][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-07-13 16:06:09.149][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-07-13 16:06:09.150][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-07-13 16:06:09.152][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-07-13 16:06:09.174][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
======
downloaded 119.1 MB
biodb.INFO [2024-07-13 16:06:58.686][biodb::testThat]
biodb.INFO [2024-07-13 16:06:58.688][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-07-13 16:06:58.689][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:58.690][biodb::testThat]
biodb.DEBUG[2024-07-13 16:06:58.699][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-07-13 16:06:58.701][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-07-13 16:06:58.703][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-07-13 16:06:58.704][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-07-13 16:06:58.705][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-07-13 16:06:58.707][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
=========
downloaded 181.4 MB
biodb.INFO [2024-07-13 16:08:14.656][biodb::testThat]
biodb.INFO [2024-07-13 16:08:14.658][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-07-13 16:08:14.659][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:08:14.661][biodb::testThat]
biodb.DEBUG[2024-07-13 16:08:14.666][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-07-13 16:08:14.668][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-07-13 16:08:14.674][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-07-13 16:08:14.676][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-07-13 16:08:14.677][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-07-13 16:08:14.682][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
===============
downloaded 273.4 MB
biodb.INFO [2024-07-13 16:11:39.332][biodb::testThat]
biodb.INFO [2024-07-13 16:11:39.333][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-13 16:11:39.334][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:11:39.336][biodb::testThat]
biodb.INFO [2024-07-13 16:11:39.346][biodb::testThat]
biodb.INFO [2024-07-13 16:11:39.347][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-13 16:11:39.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:11:39.350][biodb::testThat]
biodb.INFO [2024-07-13 16:11:39.360][biodb::testThat]
biodb.INFO [2024-07-13 16:11:39.362][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-13 16:11:39.363][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:11:39.364][biodb::testThat]
biodb.DEBUG[2024-07-13 16:11:39.368][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-07-13 16:11:51.726][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-07-13 16:11:51.960][biodb::testThat]
biodb.INFO [2024-07-13 16:11:51.962][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-13 16:11:51.963][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:11:51.964][biodb::testThat]
biodb.DEBUG[2024-07-13 16:11:52.756][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-07-13 16:11:52.841][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:11:52.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:11:52.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:11:52.845][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:11:52.847][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:11:52.848][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:11:52.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:11:52.850][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:11:52.852][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:11:52.853][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:11:52.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:11:52.855][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:11:52.857][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:11:52.858][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:11:52.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:11:52.860][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:11:52.862][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:11:52.863][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:11:52.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:11:52.865][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:11:52.867][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:11:52.868][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:11:52.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:11:52.870][ef$get] fields variable is a list.
biodb.INFO [2024-07-13 16:11:52.872][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-13 16:11:52.873][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-07-13 16:11:52.874][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-07-13 16:11:52.875][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-13 16:11:52.877][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:11:52.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:11:52.879][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:11:52.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:11:52.881][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:11:52.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 4 | WARN 8 | SKIP 0 | PASS 113 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb",
method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
3. └─conn$getBiodb()$getFactory()$getEntry(...)
4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
5. └─conn$getEntryContent(ids)
6. └─self$download()
7. └─private$doDownload()
8. └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
9. └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb",
method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
3. └─conn$getEntry(id, drop = TRUE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$download()
8. └─private$doDownload()
9. └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
10. └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb",
method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
3. └─conn$getEntry(id, drop = TRUE)
4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
6. └─conn$getEntryContent(ids)
7. └─self$download()
8. └─private$doDownload()
9. └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
10. └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb",
method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
3. └─opt$refEntries$getRealEntry(id)
4. └─self$getRealEntries(ids = id)
5. └─private$bdb$getFactory()$getEntry(...)
6. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
7. └─conn$getEntryContent(ids)
8. └─self$download()
9. └─private$doDownload()
10. └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
11. └─utils::download.file(...)
[ FAIL 4 | WARN 8 | SKIP 0 | PASS 113 ]
Error: Test failures
Execution halted
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
3. └─opt$refEntries$getRealEntry(id)
4. └─self$getRealEntries(ids = id)
5. └─private$bdb$getFactory()$getEntry(...)
6. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
7. └─conn$getEntryContent(ids)
8. └─self$download()
9. └─private$doDownload()
10. └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
11. └─utils::download.file(...)
[ FAIL 4 | WARN 8 | SKIP 0 | PASS 113 ]
Error: Test failures
Execution halted
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
* installing *source* package ‘biodbHmdb’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
accession_tag("<accession>", "</accession>"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
closed(true)
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package ‘biodbHmdb’
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)