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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ptairMS_1.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ptairMS ──────────────────────────────────────────────────────────
✔ Package installed successfully
── ptairMS session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPemOi3/file10419a520760f9/ptairMS
→ BiocVersion: 3.24
→ Package: ptairMS
→ PackageVersion: 1.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ptairMS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpPemOi3/file10419a520760f9/ptairMS
→ installDir: /tmp/RtmpPemOi3/file10419a7a5c2cba
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ptairMS ────────────────────────────────────────────────
* 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...
* 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: QualityControl
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' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (7%).
* 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:
    • ptairMS.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ptairMS...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/read_data.R (line 163, column 22)
    • R/read_data.R (line 169, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ShinnyApp.R (line 1008, column 14)
    • ShinnyApp.R (line 1074, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/Raw_Methods.R (line 301, column 9)
    • ...
    • print() in R/ShinnyApp.R (line 1183, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/alignment.R (line 36, column 11)
    • ...
    • R/ShinnyApp.R (line 1073, column 16)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/Raw_Methods.R (line 181, column 17)
    • R/SetMethods.R (line 28, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/peak_detection.R (line 1227, column 12)
  • ...
  • suppressWarnings() in R/ShinnyApp.R (line 1289, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 46
functions greater than 50 lines.
  The longest 5 functions are:
    • RunShinnyApp() (R/ShinnyApp.R): 1046 lines
    • ...
    • server() (R/app.R): 240 lines
* Checking man page documentation...
Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • RunShinnyApp.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • changeTimeLimits.Rd
    • RunShinnyApp.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • changeTimeLimits.Rd
    • RunShinnyApp.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; 1050 lines (11%) are > 80 characters long.
  First few lines:
    • R/alignment.R#L42 # Initialize variables The list who ...
    • ...
    • vignettes/ptairMS.Rmd#L468 This research was conducted by Camille R ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1942 lines (20%) are
not.
  First few lines:
    • R/alignment.R#L2 "pValGreater", ...
    • ...
    • vignettes/ptairMS.Rmd#L442 fig.pdfC = "none") ...
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 18 NOTES
ℹ See the ptairMS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.