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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('flowStats_4.24.0.tar.gz','quit-with-status'=TRUE)"
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── Installing flowStats ────────────────────────────────────────────────────────
✔ Package installed successfully
── flowStats session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpy1UPNb/file7855d38dac810/flowStats
→ BiocVersion: 3.23
→ Package: flowStats
→ PackageVersion: 4.24.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/flowStats.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmpy1UPNb/file7855d38dac810/flowStats
→ installDir: /tmp/Rtmpy1UPNb/file7855d6347dd75
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowStats ──────────────────────────────────────────────
* 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 3.0.2 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpy1UPNb/file7855d38dac810/flowStats/man/calcPBChiSquare.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpy1UPNb/file7855d38dac810/flowStats/man/calcPearsonChi.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpy1UPNb/file7855d38dac810/flowStats/man/curvPeaks.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpy1UPNb/file7855d38dac810/flowStats/man/gaussNorm.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpy1UPNb/file7855d38dac810/flowStats/man/landmarkMatrix.Rd'
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (23%).
* 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:
    • GettingStartedWithFlowStats.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GettingStartedWithFlowStats.Rnw
* Checking package installation calls in R code...
* Checking for library/require of flowStats...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/spillover.R (line 135, column 20)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/autoGate.R (line 327, column 24)
    • ...
    • R/warpSet.R (line 1082, column 52)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • autoGate.R (line 187, column 19)
    • ...
    • warpSet.R (line 1144, column 47)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/autoGate.R (line 354, column 9)
    • ...
    • print() in R/warpSet.R (line 1242, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/autoGate.R (line 103, column 6)
    • ...
    • R/warpSet.R (line 719, column 36)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/gpaSet.R (line 200, column 18)
    • ...
    • R/warpSet.R (line 716, column 37)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 55 times:
    • T in R/density1d.R (line 247, column 67)
    • ...
    • T in R/SimulateMixture.R (line 66, column 37)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • mkPriors.R (line 242, column 24)
    • ...
    • mkPriors.R (line 683, column 20)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
  • .Defunct() in R/autoGate.R (line 398, column 5)
  • .Deprecated() in R/density1d.R (line 373, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/GettingStartedWithFlowStats.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 32
functions greater than 50 lines.
  The longest 5 functions are:
    • normQA() (R/warpSet.R): 470 lines
    • ...
    • warpSet.flowSet() (R/warpSet.R): 231 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/BackGating.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/ellipse.Rd
    • ...
    • man/plotBins.Rd
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • flowClust2Prior.Rd
    • ...
    • warpSet.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 16% of man
pages use at least one of these tags.
  Found in files:
    • gate_singlet.Rd
    • ...
    • warpSet.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • gate_singlet.Rd
    • ...
    • warpSet.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; 429 lines (5%) are > 80 characters long.
  First few lines:
    • R/autoGate.R#L318 stop(sprintf("'%s' is no ...
    • ...
    • vignettes/GettingStartedWithFlowStats.Rnw#L355 For each sample, the
    results can be visu ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1917 lines (23%) contain tabs.
  First few lines:
    • R/density1d.R#L3 mmu <- missing(mu) ...
    • ...
    • vignettes/GettingStartedWithFlowStats.Rnw#L392 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2212 lines (26%) are
not.
  First few lines:
    • R/autoGate.R#L25 flowCore:::checkClass(filterId, "chara ...
    • ...
    • vignettes/GettingStartedWithFlowStats.Rnw#L405 ...
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 | ⚠ 7 WARNINGS | ℹ 16 NOTES
ℹ See the flowStats.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.