Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘metabom8/DESCRIPTION’ ... OK
* preparing ‘metabom8’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘metabom8_0.99.3.tar.gz’

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 BiocCheckGitClone('metabom8')

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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3913/1ae3cc617c74a9697dde5a00be1078076d444281/metabom8
→ BiocVersion: 3.23
→ Package: metabom8
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3913/1ae3cc617c74a9697dde5a00be1078076d444281/metabom8.BiocCheck
→ BiocCheckVersion: 1.47.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3913/1ae3cc617c74a9697dde5a00be1078076d444281/metabom8
→ 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...
── BiocCheck v1.47.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
  browseVignettes(package = 'BiocCheck')




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 R CMD CHECK

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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3913/1ae3cc617c74a9697dde5a00be1078076d444281/metabom8.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-07 10:45:24 UTC
* using option ‘--no-vignettes’
* checking for file ‘metabom8/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metabom8’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: ‘nmrdata’

The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE

Status: 1 ERROR
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/3913/1ae3cc617c74a9697dde5a00be1078076d444281/metabom8.Rcheck/00check.log’
for details.





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 BiocCheck('metabom8_0.99.3.tar.gz')

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── Installing metabom8 ─────────────────────────────────────────────────────────
✔ Package installed successfully
── metabom8 session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmph7n1mo/file2110841a23794/metabom8
→ BiocVersion: 3.23
→ Package: metabom8
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3913/1ae3cc617c74a9697dde5a00be1078076d444281/metabom8.BiocCheck
→ BiocCheckVersion: 1.47.18
→ sourceDir: /tmp/Rtmph7n1mo/file2110841a23794/metabom8
→ installDir: /tmp/Rtmph7n1mo/file211084b8a5e6f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on metabom8 ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* 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...
* 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 (5%).
* 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 metabom8...
* Checking coding practice...
* 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 40
functions greater than 50 lines.
The longest 5 functions are:
• .oplsEngine() (R/stats_fit_opls.R): 194 lines
• ...
• .plsEngine() (R/stats_fit_pls.r): 146 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 548 lines (6%) are > 80 characters long.
First few lines:
• R/00-s4_classes.R#L119 setClass("BalancedMonteCarlo", # this is ...
• ...
• vignettes/getting-started.Rmd#L477 This vignette demonstrated the core data
  ...
i NOTE: Consider multiples of 4 spaces for line indents; 2488 lines (27%) are
not.
First few lines:
• R/00-s4_classes.R#L6 slots = c( ...
• ...
• vignettes/getting-started.Rmd#L312 params) ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.47.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 4 NOTES
i See the metabom8.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.