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

To the developers/maintainers of the GenomicOZone package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicOZone.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: GenomicOZone
Version: 1.27.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GenomicOZone_1.27.0.tar.gz','quit-with-status'=TRUE)"
StartedAt: 2026-05-09 06:52:19 -0400 (Sat, 09 May 2026)
EndedAt: 2026-05-09 06:53:47 -0400 (Sat, 09 May 2026)
EllapsedTime: 88.1 seconds
RetCode: 1
Status: ERRORS
CheckDir: None
Warnings: NA
Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GenomicOZone_1.27.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing GenomicOZone ─────────────────────────────────────────────────────
✔ Package installed successfully
── GenomicOZone session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone
→ BiocVersion: 3.24
→ Package: GenomicOZone
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GenomicOZone.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone
→ installDir: /tmp/RtmpvuZALy/filea492f21976336
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GenomicOZone ───────────────────────────────────────────
* 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 4.0.0 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (38%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GenomicOZone.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/GenomicOZone.Rmd
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:37: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:94: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:41: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:110: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:25: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:64: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:93: unknown macro '\insertAllCited'
* Checking for library/require of GenomicOZone...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/MD_annotate_genes.R (line 213, column 17)
    • ...
    • R/MD_visualize_zones.R (line 305, column 54)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/MD_visualize_zones.R (line 342, column 5)
    • print() in R/MD_visualize_zones.R (line 384, column 5)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/MD_annotate_genes.R (line 14, column 10)
    • ...
    • R/MD_perform_zoning.R (line 145, column 14)
* 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 9
functions greater than 50 lines.
  The longest 5 functions are:
    • MD.Zone.Gene.path.plots() (R/MD_visualize_zones.R): 221 lines
    • ...
    • MD.Chromosome.heatmap() (R/MD_visualize_zones.R): 83 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:37: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:94: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:41: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:110: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:25: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:64: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:93: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:37: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:94: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:41: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:110: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:25: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:64: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:93: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:37: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/extract_outputs.Rd:94: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:41: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:61: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/generate_plots.Rd:110: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:25: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GenomicOZone.Rd:64: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:65: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpvuZALy/filea492f76251e0f/GenomicOZone/man/GOZDataSet.Rd:93: unknown macro '\insertAllCited'
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 139 lines (10%) are > 80 characters long.
  First few lines:
    • R/MD_annotate_genes.R#L29 if(tolower(Genome) == tolower("GRCh3 ...
    • ...
    • vignettes/GenomicOZone.Rmd#L118 Three types of plot can be generated fro
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 576 lines (40%) are
not.
  First few lines:
    • R/MD_annotate_genes.R#L11 Genomes.available <- listDatasets(useE ...
    • ...
    • vignettes/GenomicOZone.Rmd#L140 alpha = 0.05, min.effect.size ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | ℹ 13 NOTES
ℹ See the GenomicOZone.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.