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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('MSnbase_2.38.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MSnbase ──────────────────────────────────────────────────────────
✔ Package installed successfully
── MSnbase session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpHNh6AW/file8482d6406215f/MSnbase
→ BiocVersion: 3.23
→ Package: MSnbase
→ PackageVersion: 2.38.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/MSnbase.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpHNh6AW/file8482d6406215f/MSnbase
→ installDir: /tmp/RtmpHNh6AW/file8482d1fd2aaad
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MSnbase ────────────────────────────────────────────────
* 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 3.5 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpHNh6AW/file8482d6406215f/MSnbase/man/missing-data.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpHNh6AW/file8482d6406215f/MSnbase/man/readMSnSet.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Metabolomics,
SequenceMatching
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 that Package field matches directory/tarball name...
* Checking for Version: field...
✖ ERROR: Designate only one maintainer with Authors@R [cre].
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (58%).
* 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:
    • v01-MSnbase-demo.Rmd
    • v02-MSnbase-io.Rmd
    • v04-benchmarking.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/v03-MSnbase-centroiding.Rmd
    • vignettes/v04-benchmarking.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MSnbase...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/functions-OnDiskMSnExp.R (line 232, column 9)
    • require() in R/functions-OnDiskMSnExp.R (line 413, column 9)
    • require() in R/map.R (line 96, column 24)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/averageMSnSet.R (line 85, column 14)
    • ...
    • R/utils.R (line 1378, column 5)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • averageMSnSet.R (line 78, column 52)
    • ...
    • writeMSData.R (line 108, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/cache.R (line 78, column 9)
    • ...
    • cat() in R/readWriteMzTab.R (line 140, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/functions-Spectrum.R (line 752, column 20)
    • ...
    • R/methods-ReporterIons.R (line 29, column 41)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/functions-MSnSet.R (line 179, column 13)
    • ...
    • R/utils.R (line 159, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/functions-Spectrum.R (line 1090, column 14)
    • R/readMSnSet.R (line 40, column 12)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • functions-MSnSet.R (line 4, column 22)
    • ...
    • readWriteMgfData.R (line 45, column 21)
! WARNING: .Deprecated / .Defunct usage (found 14 times)
  • .Deprecated() in R/combineFeatures.R (line 36, column 9)
  • ...
  • .Defunct() in R/readWriteMzTab.R (line 155, column 26)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/Chromatogram-class.Rd
ℹ Found @ in vignettes/v01-MSnbase-demo.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 5 times)
  • <<- in R/fdata-selection.R (line 82, column 17)
  • ...
  • <<- in R/functions-MSnExp.R (line 294, column 20)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12 times)
  • suppressWarnings() in R/functions-Chromatogram.R (line 92, column 9)
  • ...
  • suppressWarnings() in R/readWriteMzTab.R (line 144, column 9)
* 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:
    • readInMemMSData() (R/readMSData.R): 211 lines
    • ...
    • .extractMultipleChromatograms() (R/functions-OnDiskMSnExp.R): 140 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/iTRAQ4.Rd
    • man/itraqdata.Rd
    • man/TMT6.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/addIdentificationData-methods.Rd
    • ...
    • man/writeMzTabData.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • compareMSnSets.Rd
  • ...
  • writeMzTabData.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:
    • MSmap-class.Rd
    • ...
    • selectFeatureData.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • MSmap-class.Rd
    • ...
    • selectFeatureData.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 373 lines (2%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L2 setGeneric("estimateNoise", function(obj ...
    • ...
    • vignettes/v05-MSnbase-development.Rmd#L158 `MSnExp`^[The *benchmarking*
    vignette co ...
ℹ NOTE: Consider 4 spaces instead of tabs; 32 lines (0%) contain tabs.
  First few lines:
    • vignettes/v03-MSnbase-centroiding.Rmd#L88 filterRt(rtr) %>% ...
    • ...
    • vignettes/v03-MSnbase-centroiding.Rmd#L359 filterMz(prol_mzr) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 5639 lines (26%) are
not.
  First few lines:
    • R/AllGenerics.R#L59 function(fnames, description, ...
    • ...
    • vignettes/v05-MSnbase-development.Rmd#L96 withSomeEve ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | ℹ 24 NOTES
ℹ See the MSnbase.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.