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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('cogena_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing cogena ───────────────────────────────────────────────────────────
✔ Package installed successfully
── cogena session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp5xHqQW/file77c6d659f5a3e/cogena
→ BiocVersion: 3.24
→ Package: cogena
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/cogena.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp5xHqQW/file77c6d659f5a3e/cogena
→ installDir: /tmp/Rtmp5xHqQW/file77c6d321f80fc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on cogena ─────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.6 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...
ℹ Bioconductor dependencies found in Imports & Depends (5%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of cogena...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/coExp.R (line 127, column 21)
    • ...
    • R/heatmapPEI.R (line 157, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • enrichment.R (line 76, column 27)
    • ...
    • sota.R (line 391, column 25)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Class_methods.R (line 124, column 5)
    • ...
    • print() in R/pClusters.R (line 48, column 23)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/clEnrich_one.R (line 71, column 19)
    • ...
    • R/upDownGene.R (line 45, column 31)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/clEnrich_one.R (line 66, column 15)
    • ...
    • R/heatmapCmap.R (line 119, column 24)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/clEnrich_one.R (line 77, column 14)
    • R/clEnrich.R (line 79, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • clEnrich_one.R (line 94, column 29)
    • heatmap.3.R (line 229, column 20)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times)
  • suppressWarnings() in R/enrichment.R (line 89, column 41)
  • ...
  • suppressWarnings() in R/pClusters.R (line 91, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
  The longest 5 functions are:
    • heatmap.3() (R/heatmap.3.R): 460 lines
    • ...
    • sota() (R/sota.R): 112 lines
* Checking man page documentation...
Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • geneclusters.Rd
  • mat.Rd
  • nClusters.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 42% of man
pages use at least one of these tags.
  Found in files:
    • coExp.Rd
    • ...
    • summary.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • coExp.Rd
    • ...
    • summary.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; 213 lines (6%) are > 80 characters long.
  First few lines:
    • R/Class_methods.R#L70 setGeneric("geneclusters", function(obje ...
    • ...
    • vignettes/cogena-vignette_pdf.Rmd#L361 [Jia, Zhilong, et al. "Cogena, a
    novel t ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 228 lines (6%) are
not.
  First few lines:
    • R/Class_methods.R#L30 function(object) return(object ...
    • ...
    • vignettes/cogena-vignette_pdf.Rmd#L297 orderMethod = "7", maintitle= ...
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 | ⚠ 1 WARNINGS | ℹ 19 NOTES
ℹ See the cogena.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.