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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('flowAI_1.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing flowAI ───────────────────────────────────────────────────────────
✔ Package installed successfully
── flowAI session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpLa87Qw/file9a7f17b26ce87/flowAI
→ BiocVersion: 3.24
→ Package: flowAI
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/flowAI.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpLa87Qw/file9a7f17b26ce87/flowAI
→ installDir: /tmp/RtmpLa87Qw/file9a7f12b0d31c6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowAI ─────────────────────────────────────────────────
* 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 4.3.0 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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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 (8%).
* 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: Evaluate more vignette chunks.
ℹ 4 out of 7 code chunks = 57% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • flowAI.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/flowAI.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpLa87Qw/file9a7f17b26ce87/flowAI/vignettes/flowAI.Rmd
* Checking package installation calls in R code...
* Checking for library/require of flowAI...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/margins.R (line 40, column 20)
    • ...
    • R/signal.R (line 136, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • anomaly-detection.R (line 76, column 36)
    • ...
    • support-qc.R (line 27, column 24)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/anomaly-detection.R (line 62, column 5)
    • ...
    • cat() in R/signal.R (line 160, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/anomaly-detection.R (line 36, column 19)
    • ...
    • R/shiny.R (line 15, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/anomaly-detection.R (line 58, column 10)
    • ...
    • R/support-qc.R (line 28, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/margins.R (line 106, column 81)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/auto-qc.R (line 316, column 35)
  • ...
  • suppressWarnings() in R/signal.R (line 99, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
  The longest 5 functions are:
    • cffilter() (R/cffilter.R): 349 lines
    • ...
    • flow_margin_check() (R/margins.R): 119 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/flow_iQC.Rd
* 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; 128 lines (7%) are > 80 characters long.
  First few lines:
    • R/anomaly-detection.R#L26 # @return \item{anoms}{Data frame contai ...
    • ...
    • vignettes/flowAI.Rmd#L156 When using the automatic method to refin ...
ℹ NOTE: Consider 4 spaces instead of tabs; 24 lines (1%) contain tabs.
  First few lines:
    • R/cffilter.R#L146 for(jj in (np-root):(np+1+root- ...
    • ...
    • R/cffilter.R#L433 ### drift = (x(n) - x(1)) / (n-1). ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 456 lines (25%) are
not.
  First few lines:
    • R/anomaly-detection.R#L37 ...
    • ...
    • vignettes/flowAI.Rmd#L28 ...
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...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the flowAI.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.