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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('flowGraph_1.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing flowGraph ────────────────────────────────────────────────────────
✔ Package installed successfully
── flowGraph session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph
→ BiocVersion: 3.24
→ Package: flowGraph
→ PackageVersion: 1.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/flowGraph.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph
→ installDir: /tmp/RtmpGnyo7G/file9c1ca56aa79f6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on flowGraph ──────────────────────────────────────────────
* 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 4.1 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...
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • flowGraph.Rmd
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph/man/fg_data_fca.Rd:31: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph/man/fg_feat_node_specenr.Rd:54: unknown macro '\insertRef'
* Checking for library/require of flowGraph...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/00_flowGraphSubset_constructor.R (line 306, column 14)
    • ...
    • R/03_flowgraph_summary.R (line 319, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/03_flowgraph_summary.R (line 148, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/00_graph.R (line 306, column 27)
    • ...
    • R/04_flowgraph_plots.R (line 1570, column 35)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 5 times)
  • <<- in R/00_flowGraphSubset_constructor.R (line 191, column 12)
  • ...
  • <<- in R/01_flowgraph_accessors.R (line 144, column 22)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/00_flowGraphSubset_constructor.R (line 143, column
  5)
  • ...
  • suppressMessages() in R/04_flowgraph_plots.R (line 1387, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 23
functions greater than 50 lines.
  The longest 5 functions are:
    • flowGraphSubset() (R/00_flowGraphSubset_constructor.R): 391 lines
    • ...
    • fg_plot() (R/04_flowgraph_plots.R): 170 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph/man/fg_data_fca.Rd:31: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph/man/fg_feat_node_specenr.Rd:54: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph/man/fg_data_fca.Rd:31: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph/man/fg_feat_node_specenr.Rd:54: unknown macro '\insertRef'
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • flowGraphSubset.Rd
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph/man/fg_data_fca.Rd:31: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpGnyo7G/file9c1ca2e938868/flowGraph/man/fg_feat_node_specenr.Rd:54: unknown macro '\insertRef'
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 1% of man
pages use at least one of these tags.
  Found in files:
    • flowGraphSubset.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • flowGraphSubset.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; 109 lines (1%) are > 80 characters long.
  First few lines:
    • R/00_flowgraph_constructor.R#L204 markers <- gsub("_","",marke ...
    • ...
    • vignettes/flowGraph.Rmd#L558 fg <- flowGraphSubset(fg_data_pos2$count ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 138 lines (2%) are
not.
  First few lines:
    • R/00_flowgraph_constructor.R#L218 whose values correspond ...
    • ...
    • vignettes/flowGraph.Rmd#L560 summary_adjust=flowGrap ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 16 NOTES
ℹ See the flowGraph.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.