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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GateFinder_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GateFinder ───────────────────────────────────────────────────────
✔ Package installed successfully
── GateFinder session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpARBkaB/filea148f58b9c630/GateFinder
→ BiocVersion: 3.24
→ Package: GateFinder
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GateFinder.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpARBkaB/filea148f58b9c630/GateFinder
→ installDir: /tmp/RtmpARBkaB/filea148f735605da
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GateFinder ─────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpARBkaB/filea148f58b9c630/GateFinder/man/LPSData.Rd'
* 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...
* 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 (29%).
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • GateFinder.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/GateFinder.Rnw
* Checking package installation calls in R code...
* Checking for library/require of GateFinder...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllMethods.R (line 650, column 14)
    • R/AllMethods.R (line 662, column 12)
    • R/AllMethods.R (line 663, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllMethods.R (line 11, column 15)
    • ...
    • AllMethods.R (line 597, column 14)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllMethods.R (line 9, column 17)
    • ...
    • R/AllMethods.R (line 577, column 8)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/AllMethods.R (line 170, column 25)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • AllMethods.R (line 583, column 16)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/GateFinder-package.Rd
ℹ Found @ in man/GateFinder.Rd
ℹ Found @ in man/GatingProjection-class.Rd
ℹ Found @ in man/plot.GateFinder.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/AllMethods.R (line 275, column 10)
  • <<- in R/AllMethods.R (line 281, column 12)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
  The longest 5 functions are:
    • GateFinder() (R/AllMethods.R): 140 lines
    • ...
    • .scoreSubSpace() (R/AllMethods.R): 62 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/GateFinder.Rd
  • man/plot.GateFinder.Rd
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/LPSData.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; 119 lines (10%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L1 ##A class which stores the identified da ...
    • ...
    • vignettes/GateFinder.Rnw#L94 \emph{plot.GateFinder()} function accept ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • man/GateFinder.Rd#L61 alpha-hull threshold for non-convex gat ...
    • man/GatingProjection-class.Rd#L38 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 394 lines (32%) are
not.
  First few lines:
    • R/AllMethods.R#L3 ...
    • ...
    • vignettes/GateFinder.Rnw#L81 xlab='Cell Length', ylab='p-p38') ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the GateFinder.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.