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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ncdfFlow_2.58.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ncdfFlow ─────────────────────────────────────────────────────────
✔ Package installed successfully
── ncdfFlow session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp46Z0K9/file84a99555783ad/ncdfFlow
→ BiocVersion: 3.23
→ Package: ncdfFlow
→ PackageVersion: 2.58.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ncdfFlow.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmp46Z0K9/file84a99555783ad/ncdfFlow
→ installDir: /tmp/Rtmp46Z0K9/file84a993de4c8cc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ncdfFlow ───────────────────────────────────────────────
* 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 2.14.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
CellBasedAssays
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 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 (50%).
* 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:
    • ncdfFlow.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ncdfFlow.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ncdfFlow.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ncdfFlow...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/ncdfIO.R (line 125, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/ncdfFlowList-methods.R (line 30, column 9)
    • ...
    • R/ncdfIO.R (line 304, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ncdfFlowSet-split-methods.R (line 100, column 42)
    • ncdfFlowSet-split-methods.R (line 149, column 39)
    • ncdfIO.R (line 102, column 37)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ncdfFlowSet-accessors.R (line 47, column 29)
    • R/ncdfFlowSet-accessors.R (line 54, column 35)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ncdfIO.R (line 73, column 25)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/extractFlowFrame.R (line 76, column 54)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/ncdfFlowSet-rbind-methods.R (line 41, column 84)
    • F in R/ncdfIO.R (line 181, column 81)
    • F in R/ncdfIO.R (line 181, column 90)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • ncdfIO.R (line 441, column 52)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/ncdfFlowList-methods.R (line 239, column 22)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • read.ncdfFlowSet() (R/ncdfIO.R): 244 lines
    • ...
    • definition() (R/subset-methods.R): 66 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/as.flowSet.Rd
    • ...
    • man/unlink-ncdfFlowSet-method.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • flowSet-accessor.Rd
    • getFileName.Rd
    • save_ncfs.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:
    • save_ncfs.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • save_ncfs.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; 226 lines (8%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L1 #' ncdfFlow: A package that provides CDF ...
    • ...
    • vignettes/ncdfFlow.Rnw#L309 same ncdf file as the original \Robject{ ...
ℹ NOTE: Consider 4 spaces instead of tabs; 666 lines (22%) contain tabs.
  First few lines:
    • R/AllClasses.R#L72 representation=representation( ...
    • ...
    • R/subset-methods.R#L85 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 558 lines (19%) are
not.
  First few lines:
    • R/AllClasses.R#L137 ...
    • ...
    • vignettes/ncdfFlow.Rnw#L228 ...
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 504 Gateway
Timeout.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 20 NOTES
ℹ See the ncdfFlow.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.