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

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

Version: 1.3.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SPICEY_1.3.0.tar.gz','quit-with-status'=TRUE)"

StartedAt: 2026-05-09 07:46:46 -0400 (Sat, 09 May 2026)

EndedAt: 2026-05-09 07:47:14 -0400 (Sat, 09 May 2026)

EllapsedTime: 28.0 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('SPICEY_1.3.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing SPICEY ───────────────────────────────────────────────────────────
✔ Package installed successfully
── SPICEY session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpuFHWyU/file14525578cf9f9/SPICEY
→ BiocVersion: 3.24
→ Package: SPICEY
→ PackageVersion: 1.3.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SPICEY.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpuFHWyU/file14525578cf9f9/SPICEY
→ installDir: /tmp/RtmpuFHWyU/file1452552f08180c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SPICEY ─────────────────────────────────────────────────
* 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...
* 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 (36%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of SPICEY...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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; 255 lines (17%) are > 80 characters long.
  First few lines:
    • R/annotate_re_genes.R#L6 #' @return A \code{data.frame} of peaks ...
    • ...
    • vignettes/SPICEY.Rmd#L532 ```{r spicey-heatmap-comb, message=FALSE ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 249 lines (17%) are
not.
  First few lines:
    • R/annotate_re_genes.R#L30 txdb, ...
    • ...
    • vignettes/SPICEY.Rmd#L536 combined_score = TRUE ...
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 4 NOTES
ℹ See the SPICEY.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.