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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('PTMods_1.1.0.tar.gz','quit-with-status'=TRUE)"
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── Installing PTMods ───────────────────────────────────────────────────────────
✔ Package installed successfully
── PTMods session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpF2JV4o/file1bbfd463edc2d9/PTMods
→ BiocVersion: 3.24
→ Package: PTMods
→ PackageVersion: 1.1.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/PTMods.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpF2JV4o/file1bbfd463edc2d9/PTMods
→ installDir: /tmp/RtmpF2JV4o/file1bbfd429abafca
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on PTMods ─────────────────────────────────────────────────
* 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: KEGG
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...
* Checking package installation calls in R code...
* Checking for library/require of PTMods...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/PTM-combine.R (line 25, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/convertAnnotation.R (line 291, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/mass.R (line 75, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/PTM-utils.R (line 193, column 20)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
  The longest 5 functions are:
    • .addVariableModifications() (R/PTM-variable.R): 78 lines
    • ...
    • .mass() (R/mass.R): 51 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; 26 lines (1%) are > 80 characters long.
  First few lines:
    • R/convertAnnotation.R#L36 #' \item Name to deltaMass: \code{"M[O ...
    • ...
    • vignettes/PTMods.Rmd#L89 [issue on the GitHub page](https://githu ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 49 lines (2%) are not.
  First few lines:
    • R/convertAnnotation.R#L78 convertToS ...
    • ...
    • vignettes/PTMods.Rmd#L147 `"M[UNIMOD:35]PEPTIDE"` for an oxidati ...
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 11 NOTES
ℹ See the PTMods.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.