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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('biomformat_1.40.0.tar.gz','quit-with-status'=TRUE)"
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── Installing biomformat ───────────────────────────────────────────────────────
✔ Package installed successfully
── biomformat session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUQz6KZ/file746ca5dbfb990/biomformat
→ BiocVersion: 3.23
→ Package: biomformat
→ PackageVersion: 1.40.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/biomformat.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpUQz6KZ/file746ca5dbfb990/biomformat
→ installDir: /tmp/RtmpUQz6KZ/file746ca2dd0e19f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on biomformat ─────────────────────────────────────────────
* 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 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: LongRead
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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...
* Checking package installation calls in R code...
* Checking for library/require of biomformat...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/BIOM-class.R (line 174, column 13)
    • ...
    • R/validity-methods.R (line 89, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • BIOM-class.R (line 522, column 16)
    • ...
    • BIOM-class.R (line 873, column 21)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/IO-methods.R (line 156, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/BIOM-class.R (line 67, column 14)
    • ...
    • R/validity-methods.R (line 97, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/IO-methods.R (line 89, column 12)
    • R/IO-methods.R (line 102, column 12)
    • R/IO-methods.R (line 373, column 7)
* 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 4
functions greater than 50 lines.
  The longest 5 functions are:
    • validbiom() (R/validity-methods.R): 104 lines
    • ...
    • _anonymous_.554() (R/BIOM-class.R): 69 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/biom_data-methods.Rd
    • man/show-methods.Rd
* 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; 99 lines (5%) are > 80 characters long.
  First few lines:
    • R/allClasses.R#L9 #' \href{http://biom-format.org/document ...
    • ...
    • vignettes/biomformat.Rmd#L155 which stores both sample-major and obser
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 184 lines (9%) contain tabs.
  First few lines:
    • R/BIOM-class.R#L64 # Some instantiation checks chould go h ...
    • ...
    • R/validity-methods.R#L110 return(TRUE) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 315 lines (15%) are
not.
  First few lines:
    • R/BIOM-class.R#L65 # or wrap them in validity methods. ...
    • ...
    • vignettes/biomformat.Rmd#L412 columns = c("Sample1", "Sa ...
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 | ⚠ 2 WARNINGS | ℹ 14 NOTES
ℹ See the biomformat.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.