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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('mzR_2.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing mzR ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── mzR session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpc01Xdz/file1ba15a15d4063d/mzR
→ BiocVersion: 3.24
→ Package: mzR
→ PackageVersion: 2.47.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/mzR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpc01Xdz/file1ba15a15d4063d/mzR
→ installDir: /tmp/Rtmpc01Xdz/file1ba15a183e2922
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mzR ────────────────────────────────────────────────────
* 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: WorkflowStep
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (43%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of mzR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/methods-mzRnetCDF.R (line 20, column 26)
    • R/utils.R (line 36, column 9)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • functions-utils.R (line 77, column 15)
    • ...
    • utils.R (line 3, column 18)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/io.R (line 178, column 34)
    • R/zzz.R (line 1, column 20)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/io.R (line 19, column 33)
    • ...
    • R/io.R (line 165, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • methods-mzRnetCDF.R (line 105, column 57)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Defunct() in R/methods-mzRpwiz.R (line 18, column 15)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Avoid 'Sys.setenv' (found 1 times)
  • Sys.setenv() in R/zzz.R (line 23, column 7)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/io.R (line 64, column 9)
  • suppressWarnings() in R/io.R (line 75, column 5)
* 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:
    • .validateHeader() (R/functions-utils.R): 69 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/copyWriteMSData.Rd
    • ...
    • man/writeMSData.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • pwiz-version.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • openMSfile.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • openMSfile.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; 24 lines (2%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L11 setGeneric("writeMSfile", function(objec ...
    • ...
    • vignettes/mzR.Rmd#L159 file <- MsDataHub::TMT_Erwinia_1uLSike_T ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • mzR/NAMESPACE#L26 isolationWindow, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 400 lines (27%) are
not.
  First few lines:
    • R/AllGenerics.R#L26 function(object, scans, ...) ...
    • ...
    • mzR/NAMESPACE#L56 "mzRident") ...
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 | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the mzR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.