Multiple platform build/check report for BioC 3.21 - CHECK results for MsBackendMetaboLights on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4461
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4403
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4358
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*

CHECK results for MsBackendMetaboLights on lconway

To the developers/maintainers of the MsBackendMetaboLights package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMetaboLights.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: MsBackendMetaboLights

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMetaboLights_1.1.0.tar.gz

StartedAt: 2024-12-02 00:02:38 -0500 (Mon, 02 Dec 2024)

EndedAt: 2024-12-02 00:09:56 -0500 (Mon, 02 Dec 2024)

EllapsedTime: 437.9 seconds

RetCode: 1

Status: ERROR

CheckDir: MsBackendMetaboLights.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMetaboLights_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MsBackendMetaboLights.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendMetaboLights/DESCRIPTION’ ... OK
* this is package ‘MsBackendMetaboLights’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘MsBackendMetaboLights’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MsBackendMetaboLights.Rd: MsBackendMzR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MsBackendMetaboLights-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MsBackendMetaboLights
> ### Title: MsBackend representing MS data from MetaboLights
> ### Aliases: MsBackendMetaboLights MsBackendMetaboLights-class
> ###   backendInitialize,MsBackendMetaboLights-method
> ###   backendMerge,MsBackendMetaboLights-method
> ###   backendRequiredSpectraVariables,MsBackendMetaboLights-method
> ###   mtbls_sync
> 
> ### ** Examples
> 
> 
> library(MsBackendMetaboLights)
> 
> ## List files of a MetaboLights data set
> mtbls_list_files("MTBLS39")
[1] "FILES"                                                                                                          
[2] "a_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry.txt"       
[3] "i_Investigation.txt"                                                                                            
[4] "m_MTBLS39_the_plasticity_of_the_grapevine_berry_transcriptome_metabolite_profiling_mass_spectrometry_v2_maf.tsv"
[5] "metexplore_mapping.json"                                                                                        
[6] "s_MTBLS39.txt"                                                                                                  
> 
> ## Initialize a MsBackendMetaboLights representing all MS data files of
> ## the data set with the ID "MTBLS39". This will download and cache all
> ## files and subsequently load and represent them in R.
> 
> be <- backendInitialize(MsBackendMetaboLights(), "MTBLS39")
Used data files from the assay's column "Raw Spectral Data File" since none were available in column "Derived Spectral Data File".
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM063C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN073C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS073C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM073C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/MN083C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/CS083C.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083A.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083B.cdf'
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS39/FILES/AM083C.cdf'
Error: database disk image is malformed
Error: database disk image is malformed
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
MetaboLights-utils 0.348   0.03   6.852
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   14.                 ├─DBI::dbExecute(conn, paste0("RELEASE SAVEPOINT ", name_quoted))
   15.                 └─DBI::dbExecute(conn, paste0("RELEASE SAVEPOINT ", name_quoted))
   16.                   ├─DBI::dbSendStatement(conn, statement, ...)
   17.                   └─DBI::dbSendStatement(conn, statement, ...)
   18.                     ├─DBI::dbSendQuery(conn, statement, ...)
   19.                     └─RSQLite::dbSendQuery(conn, statement, ...)
   20.                       └─RSQLite (local) .local(conn, statement, ...)
   21.                         ├─methods::new(...)
   22.                         │ ├─methods::initialize(value, ...)
   23.                         │ └─methods::initialize(value, ...)
   24.                         └─RSQLite:::result_create(conn@ptr, statement)
  
  [ FAIL 6 | WARN 3 | SKIP 0 | PASS 39 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/MsBackendMetaboLights.Rcheck/00check.log’
for details.

Installation output

MsBackendMetaboLights.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendMetaboLights
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘MsBackendMetaboLights’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MsBackendMetaboLights)

Tests output

MsBackendMetaboLights.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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.

> #' MetaboLights ID: MTBLS8735
> #' ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8735
> 
> library(testthat)
> library(MsBackendMetaboLights)
Loading required package: Spectra
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: BiocParallel
> 
> test_check("MsBackendMetaboLights")
[ FAIL 6 | WARN 3 | SKIP 0 | PASS 39 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_MsBackendMetaboLights.R:30:5'): backendInitialize,MsBackendMetaboLights works ──
Error: database disk image is malformed
Backtrace:
     ▆
  1. ├─ProtGenerics::backendInitialize(...) at test_MsBackendMetaboLights.R:30:5
  2. └─MsBackendMetaboLights::backendInitialize(...)
  3.   └─MsBackendMetaboLights (local) .local(object, ...)
  4.     └─MsBackendMetaboLights:::.mtbls_data_files(...)
  5.       ├─BiocFileCache::`bfcmeta<-`(...)
  6.       └─BiocFileCache::`bfcmeta<-`(...)
  7.         └─BiocFileCache:::.sql_meta_gets(x, name, value, ...)
  8.           ├─base::tryCatch(...)
  9.           │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.           ├─DBI::dbWriteTable(con, name, value, ...)
 11.           └─RSQLite::dbWriteTable(con, name, value, ...)
 12.             └─RSQLite (local) .local(conn, name, value, ...)
 13.               ├─DBI::dbRemoveTable(conn, name)
 14.               └─RSQLite::dbRemoveTable(conn, name)
 15.                 └─RSQLite (local) .local(conn, name, ...)
 16.                   ├─DBI::dbExecute(conn, paste0("DROP TABLE ", extra, name))
 17.                   └─DBI::dbExecute(conn, paste0("DROP TABLE ", extra, name))
 18.                     ├─DBI::dbSendStatement(conn, statement, ...)
 19.                     └─DBI::dbSendStatement(conn, statement, ...)
 20.                       ├─DBI::dbSendQuery(conn, statement, ...)
 21.                       └─RSQLite::dbSendQuery(conn, statement, ...)
 22.                         └─RSQLite (local) .local(conn, statement, ...)
 23.                           ├─methods::new(...)
 24.                           │ ├─methods::initialize(value, ...)
 25.                           │ └─methods::initialize(value, ...)
 26.                           └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsBackendMetaboLights.R:30:5'): backendInitialize,MsBackendMetaboLights works ──
Error: database disk image is malformed
Backtrace:
     ▆
  1. ├─ProtGenerics::backendInitialize(...) at test_MsBackendMetaboLights.R:30:5
  2. └─MsBackendMetaboLights::backendInitialize(...)
  3.   └─MsBackendMetaboLights (local) .local(object, ...)
  4.     └─MsBackendMetaboLights:::.mtbls_data_files(...)
  5.       ├─BiocFileCache::`bfcmeta<-`(...)
  6.       └─BiocFileCache::`bfcmeta<-`(...)
  7.         └─BiocFileCache:::.sql_meta_gets(x, name, value, ...)
  8.           ├─base::tryCatch(...)
  9.           │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.           ├─DBI::dbWriteTable(con, name, value, ...)
 11.           └─RSQLite::dbWriteTable(con, name, value, ...)
 12.             └─RSQLite (local) .local(conn, name, value, ...)
 13.               ├─DBI::dbRollback(conn, name = savepoint_id)
 14.               └─RSQLite::dbRollback(conn, name = savepoint_id)
 15.                 └─RSQLite (local) .local(conn, ...)
 16.                   ├─DBI::dbExecute(conn, paste0("RELEASE SAVEPOINT ", name_quoted))
 17.                   └─DBI::dbExecute(conn, paste0("RELEASE SAVEPOINT ", name_quoted))
 18.                     ├─DBI::dbSendStatement(conn, statement, ...)
 19.                     └─DBI::dbSendStatement(conn, statement, ...)
 20.                       ├─DBI::dbSendQuery(conn, statement, ...)
 21.                       └─RSQLite::dbSendQuery(conn, statement, ...)
 22.                         └─RSQLite (local) .local(conn, statement, ...)
 23.                           ├─methods::new(...)
 24.                           │ ├─methods::initialize(value, ...)
 25.                           │ └─methods::initialize(value, ...)
 26.                           └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsBackendMetaboLights.R:61:5'): mtbls_sync works ───────────────
Error: database disk image is malformed
Backtrace:
     ▆
  1. ├─BiocFileCache::cleanbfc(bfc, days = -10, ask = FALSE) at test_MsBackendMetaboLights.R:61:5
  2. └─BiocFileCache::cleanbfc(bfc, days = -10, ask = FALSE)
  3.   └─BiocFileCache:::.sql_remove_resource(x, rids)
  4.     └─BiocFileCache:::.sql_db_execute(bfc, cmd)
  5.       ├─DBI::dbExecute(con, sql, params = param)
  6.       └─DBI::dbExecute(con, sql, params = param)
  7.         ├─DBI::dbSendStatement(conn, statement, ...)
  8.         └─DBI::dbSendStatement(conn, statement, ...)
  9.           ├─DBI::dbSendQuery(conn, statement, ...)
 10.           └─RSQLite::dbSendQuery(conn, statement, ...)
 11.             └─RSQLite (local) .local(conn, statement, ...)
 12.               ├─methods::new(...)
 13.               │ ├─methods::initialize(value, ...)
 14.               │ └─methods::initialize(value, ...)
 15.               └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsBackendMetaboLights.R:96:5'): .mtbls_data_files and .mtbls_data_files_offline works ──
Error: database disk image is malformed
Backtrace:
     ▆
  1. ├─BiocFileCache::cleanbfc(bfc, days = -10, ask = FALSE) at test_MsBackendMetaboLights.R:96:5
  2. └─BiocFileCache::cleanbfc(bfc, days = -10, ask = FALSE)
  3.   └─BiocFileCache:::.sql_remove_resource(x, rids)
  4.     └─BiocFileCache:::.sql_db_execute(bfc, cmd)
  5.       ├─DBI::dbExecute(con, sql, params = param)
  6.       └─DBI::dbExecute(con, sql, params = param)
  7.         ├─DBI::dbSendStatement(conn, statement, ...)
  8.         └─DBI::dbSendStatement(conn, statement, ...)
  9.           ├─DBI::dbSendQuery(conn, statement, ...)
 10.           └─RSQLite::dbSendQuery(conn, statement, ...)
 11.             └─RSQLite (local) .local(conn, statement, ...)
 12.               ├─methods::new(...)
 13.               │ ├─methods::initialize(value, ...)
 14.               │ └─methods::initialize(value, ...)
 15.               └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsBackendMetaboLights.R:145:5'): mtbls_sync_data_files works ───
Error: database disk image is malformed
Backtrace:
     ▆
  1. └─MsBackendMetaboLights::mtbls_sync_data_files(...) at test_MsBackendMetaboLights.R:145:5
  2.   └─MsBackendMetaboLights:::.mtbls_data_files(...)
  3.     ├─BiocFileCache::`bfcmeta<-`(...)
  4.     └─BiocFileCache::`bfcmeta<-`(...)
  5.       └─BiocFileCache:::.sql_meta_gets(x, name, value, ...)
  6.         ├─base::tryCatch(...)
  7.         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.         ├─DBI::dbWriteTable(con, name, value, ...)
  9.         └─RSQLite::dbWriteTable(con, name, value, ...)
 10.           └─RSQLite (local) .local(conn, name, value, ...)
 11.             ├─DBI::dbRemoveTable(conn, name)
 12.             └─RSQLite::dbRemoveTable(conn, name)
 13.               └─RSQLite (local) .local(conn, name, ...)
 14.                 ├─DBI::dbExecute(conn, paste0("DROP TABLE ", extra, name))
 15.                 └─DBI::dbExecute(conn, paste0("DROP TABLE ", extra, name))
 16.                   ├─DBI::dbSendStatement(conn, statement, ...)
 17.                   └─DBI::dbSendStatement(conn, statement, ...)
 18.                     ├─DBI::dbSendQuery(conn, statement, ...)
 19.                     └─RSQLite::dbSendQuery(conn, statement, ...)
 20.                       └─RSQLite (local) .local(conn, statement, ...)
 21.                         ├─methods::new(...)
 22.                         │ ├─methods::initialize(value, ...)
 23.                         │ └─methods::initialize(value, ...)
 24.                         └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test_MsBackendMetaboLights.R:145:5'): mtbls_sync_data_files works ───
Error: database disk image is malformed
Backtrace:
     ▆
  1. └─MsBackendMetaboLights::mtbls_sync_data_files(...) at test_MsBackendMetaboLights.R:145:5
  2.   └─MsBackendMetaboLights:::.mtbls_data_files(...)
  3.     ├─BiocFileCache::`bfcmeta<-`(...)
  4.     └─BiocFileCache::`bfcmeta<-`(...)
  5.       └─BiocFileCache:::.sql_meta_gets(x, name, value, ...)
  6.         ├─base::tryCatch(...)
  7.         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.         ├─DBI::dbWriteTable(con, name, value, ...)
  9.         └─RSQLite::dbWriteTable(con, name, value, ...)
 10.           └─RSQLite (local) .local(conn, name, value, ...)
 11.             ├─DBI::dbRollback(conn, name = savepoint_id)
 12.             └─RSQLite::dbRollback(conn, name = savepoint_id)
 13.               └─RSQLite (local) .local(conn, ...)
 14.                 ├─DBI::dbExecute(conn, paste0("RELEASE SAVEPOINT ", name_quoted))
 15.                 └─DBI::dbExecute(conn, paste0("RELEASE SAVEPOINT ", name_quoted))
 16.                   ├─DBI::dbSendStatement(conn, statement, ...)
 17.                   └─DBI::dbSendStatement(conn, statement, ...)
 18.                     ├─DBI::dbSendQuery(conn, statement, ...)
 19.                     └─RSQLite::dbSendQuery(conn, statement, ...)
 20.                       └─RSQLite (local) .local(conn, statement, ...)
 21.                         ├─methods::new(...)
 22.                         │ ├─methods::initialize(value, ...)
 23.                         │ └─methods::initialize(value, ...)
 24.                         └─RSQLite:::result_create(conn@ptr, statement)

[ FAIL 6 | WARN 3 | SKIP 0 | PASS 39 ]
Error: Test failures
Execution halted

Example timings

MsBackendMetaboLights.Rcheck/MsBackendMetaboLights-Ex.timings

name	user	system	elapsed
MetaboLights-utils	0.348	0.030	6.852