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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('CytoML_2.24.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CytoML ───────────────────────────────────────────────────────────
✔ Package installed successfully
── CytoML session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpBxVJOJ/file75c93b6df86c/CytoML
→ BiocVersion: 3.23
→ Package: CytoML
→ PackageVersion: 2.24.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/CytoML.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpBxVJOJ/file75c93b6df86c/CytoML
→ installDir: /tmp/RtmpBxVJOJ/file75c933edea7ad
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CytoML ─────────────────────────────────────────────────
* 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 3.5.0 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...
* 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...
ℹ NOTE: License 'AGPL-3.0-only' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (36%).
* 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: Vignette(s) found with missing chunk labels
  Found in files:
    • cytobank2GatingSet.Rmd
    • flowjo_to_gatingset.Rmd
    • HowToExportGatingSet.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/cytobank2GatingSet.Rmd
    • vignettes/flowjo_to_gatingset.Rmd
    • vignettes/HowToExportGatingSet.Rmd
* Checking package installation calls in R code...
* Checking for library/require of CytoML...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/diva2GatingSet.R (line 691, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/compensation.R (line 34, column 35)
    • ...
    • R/transforms.R (line 309, column 7)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • gate-methods.R (line 494, column 32)
    • ...
    • writeGatingML.R (line 705, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/writeGatingML.R (line 74, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/compensation.R (line 15, column 22)
    • ...
    • R/writeGatingML.R (line 888, column 12)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/diva2GatingSet.R (line 476, column 17)
    • ...
    • R/writeGatingML.R (line 869, column 15)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 6 times:
    • T in R/cytobankExperiment.R (line 275, column 9)
    • ...
    • T in R/writeGatingML.R (line 484, column 32)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • flowJoWorkspace_Methods.R (line 241, column 27)
    • ...
    • read.gatingML.cytobank.R (line 253, column 19)
! WARNING: .Deprecated / .Defunct usage (found 12 times)
  • .Deprecated() in R/cytobankExperiment.R (line 17, column 3)
  • ...
  • .Deprecated() in R/GatingSet2flowJo.R (line 8, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 18 times)
  • suppressMessages() in R/diva2GatingSet.R (line 279, column 9)
  • ...
  • suppressWarnings() in R/writeGatingML.R (line 36, column 20)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 21
functions greater than 50 lines.
  The longest 5 functions are:
    • .parseDivaWorkspace() (R/diva2GatingSet.R): 422 lines
    • ...
    • export_comp_trans() (R/utils.R): 174 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/ce_get_channels.Rd
    • ...
    • man/diva_to_gatingset.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • ce_get_channels.Rd
    • ...
    • open_flowjo_xml.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 32% of man
pages use at least one of these tags.
  Found in files:
    • cytobank_to_gatingset.Rd
    • ...
    • read.gatingML.cytobank.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • cytobank_to_gatingset.Rd
    • ...
    • read.gatingML.cytobank.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; 740 lines (10%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L255 "http...www.isac.net.org.std.Gating. ...
    • ...
    • vignettes/HowToExportGatingSet.Rmd#L87 The resutled `wsp` file is a
    `XML`-based ...
ℹ NOTE: Consider 4 spaces instead of tabs; 110 lines (1%) contain tabs.
  First few lines:
    • R/cytobank2GatingSet.R#L33 trans <- getTransformations(g) ...
    • ...
    • R/writeGatingML.R#L120 stop(errMessage, call. = FALSE) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1632 lines (22%) are
not.
  First few lines:
    • R/AllClasses.R#L159 "http...www.isac.net.org.std.Gating ...
    • ...
    • vignettes/flowjo_to_gatingset.Rmd#L316 wsFile <- file.path(path,
    "no-gate.wsp" ...
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 | ⚠ 5 WARNINGS | ℹ 18 NOTES
ℹ See the CytoML.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.