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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('mzID_1.51.0.tar.gz','quit-with-status'=TRUE)"
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── Installing mzID ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── mzID session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpgkZu18/file2d1b5131aaf5f8/mzID
→ BiocVersion: 3.24
→ Package: mzID
→ PackageVersion: 1.51.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/mzID.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpgkZu18/file2d1b5131aaf5f8/mzID
→ installDir: /tmp/RtmpgkZu18/file2d1b51ccd4137
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mzID ───────────────────────────────────────────────────
* 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...
* 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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (12%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • HOWTO_mzID.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/HOWTO_mzID.Rnw
* Checking package installation calls in R code...
* Checking for library/require of mzID...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/aaa.R (line 94, column 23)
    • ...
    • R/mzIDpsm.R (line 86, column 80)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • aaa.R (line 88, column 18)
    • ...
    • mzIDpsm.R (line 198, column 46)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/mzID-constructor.R (line 75, column 17)
    • ...
    • cat() in R/mzID-constructor.R (line 101, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/mzID-constructor.R (line 65, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/aaa.R (line 367, column 40)
    • F in R/aaa.R (line 370, column 36)
    • T in R/mzID.R (line 139, column 76)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • mzIDCollection.R (line 34, column 64)
    • ...
    • mzIDCollection.R (line 274, column 34)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/aaa.R (line 128, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • mzIDpsm() (R/mzIDpsm.R): 54 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/mzID-class.Rd
    • ...
    • man/mzIDpsm-class.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • mzID-getters.Rd
    • ...
    • removeDecoy.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; 203 lines (7%) are > 80 characters long.
  First few lines:
    • R/aaa.R#L3 #' This function takes an xpath argument ...
    • ...
    • vignettes/HOWTO_mzID.Rnw#L71 \item Support for other file types cou ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 273 lines (9%) are
not.
  First few lines:
    • R/aaa.R#L341 grepl("^(http|ftp)[s]?://", x) ...
    • ...
    • vignettes/HOWTO_mzID.Rnw#L71 \item Support for other file types cou ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 12 NOTES
ℹ See the mzID.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.