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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('YAPSA_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing YAPSA ────────────────────────────────────────────────────────────
✔ Package installed successfully
── YAPSA session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpygeST0/file154b6a116a22a0/YAPSA
→ BiocVersion: 3.24
→ Package: YAPSA
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/YAPSA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpygeST0/file154b6a116a22a0/YAPSA
→ installDir: /tmp/RtmpygeST0/file154b6a33655c08
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on YAPSA ──────────────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Coverage
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...
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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (30%).
* 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:
    • vignette_confidenceIntervals.Rmd
    • ...
    • YAPSA.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/vignette_confidenceIntervals.Rmd
    • ...
    • vignettes/YAPSA.Rmd
* Checking package installation calls in R code...
* Checking for library/require of YAPSA...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/basic_functions.R (line 1301, column 46)
    • R/plot_functions.R (line 893, column 28)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • basic_functions.R (line 117, column 15)
    • ...
    • plot_functions.R (line 1202, column 47)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/basic_functions.R (line 106, column 13)
    • ...
    • cat() in R/SMC.R (line 669, column 32)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/basic_functions.R (line 327, column 21)
    • ...
    • R/plot_functions.R (line 1931, column 7)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/io_functions.R (line 59, column 13)
    • R/io_functions.R (line 60, column 13)
    • R/io_functions.R (line 61, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/basic_functions.R (line 422, column 17)
    • ...
    • R/io_functions.R (line 59, column 20)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/interact_foreign.R (line 24, column 11)
    • ...
    • system() in R/interact_foreign.R (line 415, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/confidence.R (line 307, column 17)
  • <<- in R/confidence.R (line 329, column 17)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/indel_functions.R (line 1286, column 7)
  • ...
  • suppressWarnings() in R/indel_functions.R (line 1451, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 42
functions greater than 50 lines.
  The longest 5 functions are:
    • attribution_of_indels() (R/indel_functions.R): 732 lines
    • ...
    • LCD_complex_cutoff_consensus() (R/LCD.R): 145 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/cutoffs_pcawg.Rd
    • ...
    • man/targetCapture_cor_factors.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; 41 lines (0%) are > 80 characters long.
  First few lines:
    • R/data.R#L68 #' @source \code{AlexInitial}: \url{ftp: ...
    • ...
    • vignettes/YAPSA.Rmd#L1080 topic explained in a separate [vignette] ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2892 lines (21%) are
not.
  First few lines:
    • R/confidence.R#L25 in_bac ...
    • ...
    • vignettes/YAPSA.Rmd#L1141 in_subgroup_co ...
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 20 NOTES
ℹ See the YAPSA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.