Rapid builds (Linux only) of a subset of BioC 3.23<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-22 r89945) -- "Because it was There"	923
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 VisiumIO on teran2

To the developers/maintainers of the VisiumIO 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.

raw results

Summary

Package: VisiumIO

Version: 1.8.0

Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('VisiumIO_1.8.0.tar.gz','quit-with-status'=TRUE)"

StartedAt: 2026-05-07 15:48:27 -0400 (Thu, 07 May 2026)

EndedAt: 2026-05-07 15:49:05 -0400 (Thu, 07 May 2026)

EllapsedTime: 37.9 seconds

RetCode: 0

Status: OK

CheckDir: None

Warnings: 0

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('VisiumIO_1.8.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing VisiumIO ─────────────────────────────────────────────────────────
✔ Package installed successfully
── VisiumIO session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpmLKN5k/file9a2e67377c39d/VisiumIO
→ BiocVersion: 3.23
→ Package: VisiumIO
→ PackageVersion: 1.8.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/VisiumIO.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpmLKN5k/file9a2e67377c39d/VisiumIO
→ installDir: /tmp/RtmpmLKN5k/file9a2e64c213a21
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on VisiumIO ───────────────────────────────────────────────
* 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 4.5.0 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:
MultipleComparison
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 (73%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • VisiumIO.Rmd
* Checking package installation calls in R code...
* Checking for library/require of VisiumIO...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • utilities.R (line 226, column 49)
* 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 3
functions greater than 50 lines.
  The longest 5 functions are:
    • TENxVisiumHD() (R/TENxVisiumHD-class.R): 119 lines
    • TENxVisium() (R/TENxVisium-class.R): 64 lines
    • TENxVisiumList() (R/TENxVisiumList-class.R): 60 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; 4 lines (0%) are > 80 characters long.
  First few lines:
    • R/TENxGeoJSON.R#L25 #' @seealso <https://www.10xgenomics.com ...
    • ...
    • vignettes/VisiumIO.Rmd#L87 Note that we use the `images = "lowres"` ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 7 NOTES
ℹ See the VisiumIO.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.