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

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

Version: 1.1.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('fRagmentomics_1.1.0.tar.gz','quit-with-status'=TRUE)"

StartedAt: 2026-05-09 06:49:23 -0400 (Sat, 09 May 2026)

EndedAt: 2026-05-09 06:50:40 -0400 (Sat, 09 May 2026)

EllapsedTime: 77.1 seconds

RetCode: 0

Status: OK

CheckDir: None

Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('fRagmentomics_1.1.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing fRagmentomics ────────────────────────────────────────────────────
✔ Package installed successfully
── fRagmentomics session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp5tJwAy/file9e31216ae300b/fRagmentomics
→ BiocVersion: 3.24
→ Package: fRagmentomics
→ PackageVersion: 1.1.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/fRagmentomics.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp5tJwAy/file9e31216ae300b/fRagmentomics
→ installDir: /tmp/Rtmp5tJwAy/file9e3122e697050
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on fRagmentomics ──────────────────────────────────────────
* 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...
* 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 (32%).
* 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 fRagmentomics...
* 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 19
functions greater than 50 lines.
  The longest 5 functions are:
    • plot_motif_barplot() (R/plot_motif_barplot.R): 383 lines
    • ...
    • get_mutation_status_of_read() (R/get_mutation_status_of_read.R): 277
    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; 356 lines (6%) are > 80 characters long.
  First few lines:
    • R/extract_fragment_features.R#L59 fragment_qc, sample_id, chr, pos, ...
    • ...
    • vignettes/fRagmentomics.Rmd#L493 This section provides details about the
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1996 lines (34%) are
not.
  First few lines:
    • R/apply_bcftools_norm.R#L6 bcftools_path <- Sys.which("bcftools") ...
    • ...
    • vignettes/fRagmentomics.Rmd#L487 alpha = 0.7 ...
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 6 NOTES
ℹ See the fRagmentomics.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.