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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('flowWorkspace_4.24.0.tar.gz','quit-with-status'=TRUE)"
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── Installing flowWorkspace ────────────────────────────────────────────────────
✔ Package installed successfully
── flowWorkspace session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmpiQRmrD/file7904c7acbf58f/flowWorkspace
→ BiocVersion: 3.23
→ Package: flowWorkspace
→ PackageVersion: 4.24.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/flowWorkspace.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpiQRmrD/file7904c7acbf58f/flowWorkspace
→ installDir: /tmp/RtmpiQRmrD/file7904c3b5f12cf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowWorkspace ──────────────────────────────────────────
* 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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (38%).
* 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:
    • flowWorkspace-Introduction.Rmd
    • HowToMergeGatingSet.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/flowWorkspace-Introduction.Rmd
    • vignettes/HowToMergeGatingSet.Rmd
* Checking package installation calls in R code...
* Checking for library/require of flowWorkspace...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/add_Methods.R (line 121, column 13)
    • ...
    • R/utils.R (line 27, column 10)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • add_Methods.R (line 233, column 39)
    • ...
    • merge_GatingSet.R (line 214, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/utils.R (line 49, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/cytoframe.R (line 890, column 18)
    • ...
    • R/utils.R (line 86, column 16)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/load_gs.R (line 132, column 53)
    • R/merge_gslist.R (line 29, column 11)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/GatingSet_Methods.R (line 288, column 83)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 13 times:
    • T in R/flow_trans.R (line 431, column 5)
    • ...
    • T in R/utils.R (line 27, column 88)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • cytoset.R (line 912, column 17)
    • ...
    • merge_gslist.R (line 78, column 17)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/load_gs.R (line 185, column 5)
    • system() in R/load_gs.R (line 187, column 5)
! WARNING: .Deprecated / .Defunct usage (found 62 times)
  • .Deprecated() in R/add_Methods.R (line 15, column 25)
  • ...
  • .Deprecated() in R/utils.R (line 87, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/cf_append_cols.Rd
ℹ Found @ in vignettes/flowWorkspace-Introduction.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 21 times)
  • <<- in R/GatingHierarchy_Methods.R (line 65, column 17)
  • ...
  • <<- in R/GatingHierarchy_Methods.R (line 164, column 14)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11 times)
  • suppressMessages() in R/AllClasses.R (line 152, column 11)
  • ...
  • suppressMessages() in R/load_gs.R (line 340, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
  The longest 5 functions are:
    • .graph_handler() (R/GatingHierarchy_Methods.R): 151 lines
    • ...
    • .mergeGates() (R/GatingHierarchy_Methods.R): 94 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/booleanFilter-class.Rd
    • ...
    • man/transformerList.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • cf_get_uri.Rd
    • ...
    • transform.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 35% of man
pages use at least one of these tags.
  Found in files:
    • compensate.Rd
    • ...
    • transform.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • compensate.Rd
    • ...
    • transform.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; 922 lines (8%) are > 80 characters long.
  First few lines:
    • R/add_Methods.R#L20 #' Create a GatingSet and add/remove the ...
    • ...
    • vignettes/HowToMergeGatingSet.Rmd#L204 Sometime there may be the extra
    `channel ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1238 lines (11%) contain tabs.
  First few lines:
    • R/add_Methods.R#L14 { ...
    • ...
    • vignettes/HowToMergeGatingSet.Rmd#L37 **...** other arguments ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2141 lines (20%) are
not.
  First few lines:
    • R/add_Methods.R#L118 ...
    • ...
    • vignettes/HowToMergeGatingSet.Rmd#L172 for(gs in gs_groups[[i]]) ...
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 23 NOTES
ℹ See the flowWorkspace.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.