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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MutSeqR_1.1.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MutSeqR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── MutSeqR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpV1GSW6/filef476a2cbe7672/MutSeqR
→ BiocVersion: 3.24
→ Package: MutSeqR
→ PackageVersion: 1.1.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MutSeqR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpV1GSW6/filef476a2cbe7672/MutSeqR
→ installDir: /tmp/RtmpV1GSW6/filef476a7f7c71b8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MutSeqR ────────────────────────────────────────────────
* 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 (43%).
* 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 MutSeqR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/spectra_comparison_rpdmm.R (line 251, column 5)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • proast.min.R (line 262, column 24)
    • ...
    • write_nice_excel.R (line 128, column 16)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/calculate_mf.R (line 497, column 50)
    • ...
    • print() in R/proast.min.R (line 15088, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/import_helpers.R (line 47, column 17)
    • ...
    • R/spectra_comparison_G2stat.R (line 210, column 11)
* 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 86
functions greater than 50 lines.
  The longest 5 functions are:
    • f.select.m5.con() (R/proast.min.R): 1436 lines
    • ...
    • f.nlminb() (R/proast.min.R): 721 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • render_report.Rd
  • ...
  • spectra_comparison_rpdmm.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • signature_fitting.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; 888 lines (3%) are > 80 characters long.
  First few lines:
    • R/calculate_mf.R#L485 dplyr::group_by(dplyr::a ...
    • ...
    • vignettes/MutSeqR_introduction.Rmd#L1448 If an experimental variable is
    not provi ...
ℹ NOTE: Consider 4 spaces instead of tabs; 10 lines (0%) contain tabs.
  First few lines:
    • R/model_mf.R#L107 #' 25:chr1 0:chr1 ...
    • ...
    • R/spectra_comparison_G2stat.R#L62 #' 50:bone_marrow 50:liver ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 6463 lines (24%) are
not.
  First few lines:
    • R/bmd_proast.R#L192 stop("Package \"withr\" needed for ...
    • ...
    • vignettes/MutSeqR_introduction.Rmd#L1442 Also includes recurrent
    mutations wit ...
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 12 NOTES
ℹ See the MutSeqR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.