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R CMD BUILD
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* checking for file ‘MetaboAnnotatoR/DESCRIPTION’ ... OK
* preparing ‘MetaboAnnotatoR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘MetaboAnnotatoR_0.99.16.tar.gz’
===============================
BiocCheckGitClone('MetaboAnnotatoR')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/54c98252333644e2e87e8df637e8df0962a88577/MetaboAnnotatoR
→ BiocVersion: 3.23
→ Package: MetaboAnnotatoR
→ PackageVersion: 0.99.16
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/54c98252333644e2e87e8df637e8df0962a88577/MetaboAnnotatoR.BiocCheck
→ BiocCheckVersion: 1.47.16
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/54c98252333644e2e87e8df637e8df0962a88577/MetaboAnnotatoR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
! WARNING: Unable to read CITATION file with 'utils::readCitationFile()'
── BiocCheck v1.47.16 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4016/54c98252333644e2e87e8df637e8df0962a88577/MetaboAnnotatoR.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaboAnnotatoR/DESCRIPTION’ ... OK
* this is package ‘MetaboAnnotatoR’ version ‘0.99.16’
* 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 ‘MetaboAnnotatoR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [14s/14s] OK
* checking whether startup messages can be suppressed ... [13s/13s] OK
* checking use of S3 registration ... 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 ... [43s/43s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [14s/14s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [78s/174s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotateAIF 26.167 5.080 69.660
getPseudoMSMS 11.922 2.545 72.014
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/8s]
[8s/8s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(MetaboAnnotatoR)
Loading required package: xcms
Loading required package: BiocParallel
Error: package or namespace load failed for 'xcms' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'MSnbase'
Error: package 'xcms' could not be loaded
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 ... [4s/4s] OK
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4016/54c98252333644e2e87e8df637e8df0962a88577/MetaboAnnotatoR.Rcheck/00check.log’
for details.
===============================
BiocCheck('MetaboAnnotatoR_0.99.16.tar.gz')
===============================
── Installing MetaboAnnotatoR ──────────────────────────────────────────────────
✔ Package installed successfully
── MetaboAnnotatoR session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpSwzGwu/file3e4a2f2d64fbc5/MetaboAnnotatoR
→ BiocVersion: 3.23
→ Package: MetaboAnnotatoR
→ PackageVersion: 0.99.16
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/54c98252333644e2e87e8df637e8df0962a88577/MetaboAnnotatoR.BiocCheck
→ BiocCheckVersion: 1.47.16
→ sourceDir: /tmp/RtmpSwzGwu/file3e4a2f2d64fbc5/MetaboAnnotatoR
→ installDir: /tmp/RtmpSwzGwu/file3e4a2f151caeb6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MetaboAnnotatoR ────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.5.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
i NOTE: Consider adding these automatically suggested biocViews: Proteomics,
ImmunoOncology, QualityControl, DataImport
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (60%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MetaboAnnotatoR...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/getPseudoMSMS.R (line 384, column 5)
• cat() in R/getPseudoMSMS.R (line 389, column 9)
• cat() in R/getPseudoMSMS.R (line 392, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
The longest 5 functions are:
• annotateAIF() (R/annotateAIF.R): 190 lines
• ...
• plotPseudoMSMS() (R/getPseudoMSMS.R): 94 lines
* Checking man page documentation...
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘xcms’
Calls: BiocCheck ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted