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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('flowClust_3.50.0.tar.gz','quit-with-status'=TRUE)"
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── Installing flowClust ────────────────────────────────────────────────────────
✔ Package installed successfully
── flowClust session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpcg6KuU/file782c1240374c2/flowClust
→ BiocVersion: 3.23
→ Package: flowClust
→ PackageVersion: 3.50.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/flowClust.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmpcg6KuU/file782c1240374c2/flowClust
→ installDir: /tmp/Rtmpcg6KuU/file782c16b35194e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowClust ──────────────────────────────────────────────
* 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 2.5.0 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: Bayesian
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: 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 (57%).
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/flowClust.Rmd
* Checking package installation calls in R code...
* Checking for library/require of flowClust...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/flowClust.R (line 673, column 15)
    • R/SetClasses.R (line 32, column 32)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • flowClust.R (line 296, column 27)
    • ...
    • split.R (line 109, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/flowClust.R (line 468, column 41)
    • ...
    • cat() in R/SetMethods.R (line 455, column 15)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/flowClust.R (line 310, column 17)
    • ...
    • R/miscellaneous.R (line 240, column 24)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/flowClust.R (line 288, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 35 times:
    • T in R/flowClust.R (line 575, column 61)
    • ...
    • F in R/SetMethods.R (line 493, column 105)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • flowClust.R (line 483, column 79)
    • ...
    • flowClust.R (line 748, column 23)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/flowClust.R (line 572, column 35)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • .flowClustK() (R/flowClust.R): 422 lines
    • ...
    • getEstimates() (R/miscellaneous.R): 69 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/flowClust.den.Rd
    • ...
    • man/tmixFilter.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • dmvt.Rd
    • ...
    • summary.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; 151 lines (4%) are > 80 characters long.
  First few lines:
    • R/coerce.R#L33 new("tmixFilterResultList", from, ...
    • ...
    • vignettes/flowClust.Rmd#L246 The parameter `kappa` acts as a weightin ...
ℹ NOTE: Consider 4 spaces instead of tabs; 593 lines (17%) contain tabs.
  First few lines:
    • R/flowClust.R#L253 if (is(x, "flowFrame")) { ...
    • ...
    • vignettes/flowClust.Rmd#L262 ) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 527 lines (16%) are
not.
  First few lines:
    • R/coerce.R#L15 new("tmixFilterResult", from, subS ...
    • ...
    • vignettes/flowClust.Rmd#L71 blas='-L/usr/local/mkl/lib/em64t/ -lmk ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 15 NOTES
ℹ See the flowClust.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.