Build/check report for BioC 3.24 - BIOCCHECK results for transmogR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4890
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*

BIOCCHECK results for transmogR on nebbiolo2

To the developers/maintainers of the transmogR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/transmogR.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: transmogR

Version: 1.9.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('transmogR_1.9.0.tar.gz','quit-with-status'=TRUE)"

StartedAt: 2026-05-09 07:53:06 -0400 (Sat, 09 May 2026)

EndedAt: 2026-05-09 07:54:13 -0400 (Sat, 09 May 2026)

EllapsedTime: 67.1 seconds

RetCode: 0

Status: OK

CheckDir: None

Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('transmogR_1.9.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
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── Installing transmogR ────────────────────────────────────────────────────────
✔ Package installed successfully
── transmogR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0nTrkx/file14efaa3278f9b3/transmogR
→ BiocVersion: 3.24
→ Package: transmogR
→ PackageVersion: 1.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/transmogR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp0nTrkx/file14efaa3278f9b3/transmogR
→ installDir: /tmp/Rtmp0nTrkx/file14efaa65c871ee
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on transmogR ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.1.0 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: Coverage,
SequenceMatching, 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 if 'Package:' field matches directory / tarball...
* 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 (50%).
* 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 package installation calls in R code...
* Checking for library/require of transmogR...
* 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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • digestSalmon() (R/digestSalmon.R): 131 lines
    • ...
    • _anonymous_.72() (R/indelcator.R): 59 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; 46 lines (2%) are > 80 characters long.
  First few lines:
    • R/cleanVariants.R#L26 #' @param ol_vars Error handling for any ...
    • ...
    • vignettes/creating_a_new_reference.Rmd#L290 Whilst some common-use
    laptops may have ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1 lines (0%) are not.
  First few lines:
    • vignettes/creating_a_new_reference.Rmd#L63
    install.packages("BiocManager") ...
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 for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 7 NOTES
ℹ See the transmogR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.