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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('mspms_1.5.0.tar.gz','quit-with-status'=TRUE)"
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── Installing mspms ────────────────────────────────────────────────────────────
✔ Package installed successfully
── mspms session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4bRzRp/filee75c07dca1acc/mspms
→ BiocVersion: 3.24
→ Package: mspms
→ PackageVersion: 1.5.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/mspms.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp4bRzRp/filee75c07dca1acc/mspms
→ installDir: /tmp/Rtmp4bRzRp/filee75c039d3fdaf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mspms ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.4.0 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 (17%).
* 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:
    • mspms_vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of mspms...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/limma_stats.R (line 57, column 16)
    • ...
    • R/preprocessing_helper_functions.R (line 729, column 19)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • preprocessing_helper_functions.R (line 219, column 19)
    • preprocessing_helper_functions.R (line 311, column 19)
    • preprocessing_helper_functions.R (line 716, column 56)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/limma_stats.R (line 42, column 15)
* 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 2
functions greater than 50 lines.
  The longest 5 functions are:
    • limma_stats() (R/limma_stats.R): 72 lines
    • prepared_to_qf() (R/preprocessing_helper_functions.R): 63 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • pipe.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; 43 lines (1%) are > 80 characters long.
  First few lines:
    • R/limma_stats.R#L79 dplyr::select("condition", "peptide" ...
    • ...
    • vignettes/mspms_vignette.Rmd#L393 This makes the data easy to manipulate
    p ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 966 lines (30%) are
not.
  First few lines:
    • R/calculate_all_cleavages.R#L17 # calculate the length of the peptides
    ...
    • ...
    • vignettes/mspms_vignette.Rmd#L511 plot_time_course() ...
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 mspms.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.