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

To the developers/maintainers of the ANCOMBC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ANCOMBC.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: ANCOMBC
Version: 2.15.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ANCOMBC_2.15.0.tar.gz','quit-with-status'=TRUE)"
StartedAt: 2026-05-09 06:17:11 -0400 (Sat, 09 May 2026)
EndedAt: 2026-05-09 06:18:00 -0400 (Sat, 09 May 2026)
EllapsedTime: 49.0 seconds
RetCode: 0
Status: WARNINGS
CheckDir: None
Warnings: 1
Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ANCOMBC_2.15.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing ANCOMBC ──────────────────────────────────────────────────────────
✔ Package installed successfully
── ANCOMBC session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC
→ BiocVersion: 3.24
→ Package: ANCOMBC
→ PackageVersion: 2.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ANCOMBC.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC
→ installDir: /tmp/RtmpgbduWy/file541027f8450d3
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ANCOMBC ────────────────────────────────────────────────
* 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: Regression,
StructuralEquationModels, GO
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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • ANCOM.Rmd
    • ...
    • SECOM.Rmd
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancom.Rd:204: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancom.Rd:206: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc.Rd:234: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc.Rd:236: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:402: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:404: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:406: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:408: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:410: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:412: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:414: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/sim_plnm.Rd:66: unknown macro '\insertRef'
* Checking for library/require of ANCOMBC...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/data_sanity_check.R (line 355, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ancom.R (line 170, column 7)
    • ...
    • R/utils.R (line 187, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/data_sanity_check.R (line 124, column 17)
    • ...
    • R/data_sanity_check.R (line 263, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 17 times)
  • suppressWarnings() in R/ancom.R (line 348, column 30)
  • ...
  • suppressWarnings() in R/sparse_linear.R (line 132, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
  The longest 5 functions are:
    • .ancombc2_core() (R/ancombc_prep.R): 316 lines
    • ...
    • data_sanity_check() (R/data_sanity_check.R): 274 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancom.Rd:204: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancom.Rd:206: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc.Rd:234: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc.Rd:236: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:402: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:404: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:406: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:408: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:410: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:412: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:414: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/sim_plnm.Rd:66: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancom.Rd:204: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancom.Rd:206: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc.Rd:234: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc.Rd:236: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:402: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:404: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:406: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:408: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:410: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:412: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:414: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/sim_plnm.Rd:66: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancom.Rd:204: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancom.Rd:206: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc.Rd:234: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc.Rd:236: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:402: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:404: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:406: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:408: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:410: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:412: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/ancombc2.Rd:414: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpgbduWy/file541024762ef85/ANCOMBC/man/sim_plnm.Rd:66: unknown macro '\insertRef'
* 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; 239 lines (3%) are > 80 characters long.
  First few lines:
    • R/ancom.R#L30 #' \code{matrix}, \code{data.frame}, \co ...
    • ...
    • vignettes/SECOM.Rmd#L617 aggregate_data ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1523 lines (20%) are
not.
  First few lines:
    • R/ancom.R#L171 assay.type = NULL, assa ...
    • ...
    • vignettes/SECOM.Rmd#L633 thresh_hard = 0.3, ...
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 | ⚠ 1 WARNINGS | ℹ 12 NOTES
ℹ See the ANCOMBC.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.