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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('flowDensity_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing flowDensity ──────────────────────────────────────────────────────
✔ Package installed successfully
── flowDensity session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpEPU3Sl/file9b551db6143b/flowDensity
→ BiocVersion: 3.24
→ Package: flowDensity
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/flowDensity.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpEPU3Sl/file9b551db6143b/flowDensity
→ installDir: /tmp/RtmpEPU3Sl/file9b5516ff03ca4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowDensity ────────────────────────────────────────────
* 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...
! WARNING: Use biocViews from one category only (one of Software,
ExperimentData, AnnotationData, Workflow)
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...
* 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 (22%).
* 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
✖ ERROR: 'VignetteEngine' specified but not in the DESCRIPTION.
  Add 'VignetteEngine' to DESCRIPTION from the following:
    • vignettes/flowDensity.Rmd
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • vignette: "%\\VignetteEngine{knitr
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • flowDensity.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/flowDensity.Rmd (chunk no. 2, line 91, column 66)
    • ...
    • vignettes/flowDensity.Rmd (chunk no. 16, line 333, column 55)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/flowDensity.Rmd
* Checking package installation calls in R code...
* Checking for library/require of flowDensity...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • helper_functions.R (line 73, column 12)
    • ...
    • helper_functions.R (line 554, column 12)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • helper_functions.R (line 871, column 43)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/helper_functions.R (line 54, column 8)
    • ...
    • print() in R/helper_functions.R (line 905, column 5)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 75 times:
    • T in R/flowDensity_methods.R (line 155, column 49)
    • ...
    • F in R/openCyto_wrappers.R (line 59, column 69)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • flowDensity_methods.R (line 66, column 17)
    • ...
    • helper_functions.R (line 539, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/notSubFrame.Rd
ℹ Found @ in vignettes/flowDensity.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/helper_functions.R (line 567, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
  The longest 5 functions are:
    • .deGate2D() (R/helper_functions.R): 181 lines
    • ...
    • .getScoreIndex() (R/helper_functions.R): 88 lines
* Checking man page documentation...
* Checking package NEWS...
* 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; 343 lines (15%) are > 80 characters long.
  First few lines:
    • R/flowDensity_methods.R#L11 .deGate2D(f=obj@flow.frame, ...
    • ...
    • vignettes/flowDensity.Rmd#L328 It is possible to overlay density curves
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 70 lines (3%) contain tabs.
  First few lines:
    • R/AllClasses.R#L12 index="numeric")) ...
    • ...
    • vignettes/flowDensity.Rmd#L308 * `slope.w`: Sets window.width for trac
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1109 lines (47%) are
not.
  First few lines:
    • R/AllClasses.R#L6 ...
    • ...
    • vignettes/flowDensity.Rmd#L183 tmp.cp2@gates[2]), ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 5 ERRORS | ⚠ 5 WARNINGS | ℹ 14 NOTES
ℹ See the flowDensity.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.