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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('flowPeaks_1.59.0.tar.gz','quit-with-status'=TRUE)"
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── Installing flowPeaks ────────────────────────────────────────────────────────
✔ Package installed successfully
── flowPeaks session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4Y7av0/file9c6126778e1de/flowPeaks
→ BiocVersion: 3.24
→ Package: flowPeaks
→ PackageVersion: 1.59.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/flowPeaks.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp4Y7av0/file9c6126778e1de/flowPeaks
→ installDir: /tmp/Rtmp4Y7av0/file9c6127aa46da8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowPeaks ──────────────────────────────────────────────
* 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 2.12.0 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...
! WARNING: Invalid BiocViews term(s):
  • 'Gating'
* Checking for recommended biocViews...
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
ℹ NOTE: License 'Artistic-1.0' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 1-12-2012
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • flowPeaks-guide.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/flowPeaks-guide.Rnw
* Checking package installation calls in R code...
* Checking for library/require of flowPeaks...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/flowPeaks.R (line 102, column 9)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • flowPeaks.R (line 46, column 14)
    • ...
    • flowPeaks.R (line 645, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/flowPeaks.R (line 643, column 5)
    • F in R/flowPeaks.R (line 646, column 13)
    • F in R/flowPeaks.R (line 649, column 15)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • flowPeaks.R (line 316, column 17)
    • flowPeaks.R (line 343, column 21)
    • flowPeaks.R (line 446, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/flowPeaks-guide.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/flowPeaks.R (line 363, column 11)
* 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:
    • plot.flowPeaks() (R/flowPeaks.R): 122 lines
    • process.flowPeaks() (R/flowPeaks.R): 59 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/evalCluster.Rd
    • ...
    • man/summary.flowPeaks.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • adjust.flowPeaks.Rd
    • assign.flowPeaks.Rd
    • evalCluster.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
  Found in files:
    • flowPeaks.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • flowPeaks.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...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 62 lines (5%) are > 80 characters long.
  First few lines:
    • R/flowPeaks.R#L31 stop("the setting for ",deparse( ...
    • ...
    • vignettes/flowPeaks-guide.Rnw#L215 expression slot of the flowFrame where
    o ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 166 lines (13%) are
not.
  First few lines:
    • R/flowPeaks.R#L78 matrix(res$site[1:(2*nedge)],n ...
    • ...
    • vignettes/flowPeaks-guide.Rnw#L218 \centering ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 6 WARNINGS | ℹ 18 NOTES
ℹ See the flowPeaks.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.