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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('flowViz_1.76.0.tar.gz','quit-with-status'=TRUE)"
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── Installing flowViz ──────────────────────────────────────────────────────────
✔ Package installed successfully
── flowViz session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpG7Hcbk/file78e8b6b90e0ea/flowViz
→ BiocVersion: 3.23
→ Package: flowViz
→ PackageVersion: 1.76.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/flowViz.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpG7Hcbk/file78e8b6b90e0ea/flowViz
→ installDir: /tmp/RtmpG7Hcbk/file78e8b5d5a8dce
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowViz ────────────────────────────────────────────────
* 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 2.7.0 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...
* 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 (11%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • filters.Rmd
✖ ERROR: No 'VignetteEngine' specified in vignette.
  Add 'VignetteEngine' to the following files:
    • vignettes/densityplot_vs_histogram.Rmd
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • filters.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • densityplot_vs_histogram.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/densityplot_vs_histogram.Rmd (chunk no. 4, line 45, column 30)
    • ...
    • vignettes/densityplot_vs_histogram.Rmd (chunk no. 8, line 96, column 84)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/densityplot_vs_histogram.Rmd
    • vignettes/filters.Rmd
* Checking package installation calls in R code...
* Checking for library/require of flowViz...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/addNames-methods.R (line 266, column 18)
    • ...
    • R/xyplot.R (line 1448, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • addNames-methods.R (line 108, column 45)
    • ...
    • xyplot.R (line 1152, column 39)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/densityplot.R (line 488, column 12)
    • ...
    • R/splom.R (line 112, column 20)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/densityplot.R (line 856, column 57)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • flowPlot.R (line 90, column 50)
    • ...
    • xyplot.R (line 1002, column 35)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/timeLinePlot.R (line 114, column 9)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/gateplotting_utils.R (line 417, column 3)
* 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 16
functions greater than 50 lines.
  The longest 5 functions are:
    • panel.xyplot.flowframe() (R/xyplot.R): 317 lines
    • ...
    • _anonymous_.61() (R/flowPlot.R): 173 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/contour-methods.Rd
    • ...
    • man/xyplot.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addName-methods.Rd
    • ...
    • plot.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • lattice-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • lattice-methods.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; 185 lines (2%) are > 80 characters long.
  First few lines:
    • R/addNames-methods.R#L67 #' @param pos,abs specifying location of ...
    • ...
    • vignettes/filters.Rmd#L629 ```{r plotparCoord, fig=TRUE, include=FA ...
ℹ NOTE: Consider 4 spaces instead of tabs; 417 lines (5%) contain tabs.
  First few lines:
    • R/addNames-methods.R#L74 # browser() ...
    • ...
    • vignettes/filters.Rmd#L280 ) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2538 lines (30%) are
not.
  First few lines:
    • R/addNames-methods.R#L71 signature(x="rectangleGate", n ...
    • ...
    • vignettes/filters.Rmd#L579 ...
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 ───────────────────────────────────────────────────
✖ 5 ERRORS | ⚠ 8 WARNINGS | ℹ 15 NOTES
ℹ See the flowViz.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.