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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Cogito_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Cogito ───────────────────────────────────────────────────────────
✔ Package installed successfully
── Cogito session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvA6XNQ/file77cf229fc0645/Cogito
→ BiocVersion: 3.24
→ Package: Cogito
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Cogito.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvA6XNQ/file77cf229fc0645/Cogito
→ installDir: /tmp/RtmpvA6XNQ/file77cf22260dab
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Cogito ─────────────────────────────────────────────────
* 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 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvA6XNQ/file77cf229fc0645/Cogito/man/MurEpi.ChIP.small.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvA6XNQ/file77cf229fc0645/Cogito/man/MurEpi.RNA.small.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpvA6XNQ/file77cf229fc0645/Cogito/man/MurEpi.RRBS.small.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Coverage
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 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 (31%).
* 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 Cogito...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/function_aggregateRanges.R (line 233, column 13)
    • ...
    • cat() in R/function_aggregateRanges.R (line 245, column 9)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • summarizeRanges() (R/function_summarizeRanges.R): 796 lines
    • ...
    • Cgt.plotAttributeCont() (R/function_summarizeRanges.R): 184 lines
* Checking man page documentation...
* Checking package NEWS...
! WARNING: news(package='Cogito') failed with news file: Cogito/NEWS.md:news()
failed to parse news file: Cogito/NEWS.md Refer to
https://contributions.bioconductor.org/news.html to be included in Bioconductor
release announcements.
* 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; 1 lines (0%) are > 80 characters long.
  First few lines:
    • vignettes/Cogito.Rmd#L167 The main result is the report about the ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 13 lines (0%) are not.
  First few lines:
    • R/function_aggregateRanges.R#L219 functi ...
    • ...
    • R/function_summarizeRanges.R#L1453 gsub("[[: ...
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 11 NOTES
ℹ See the Cogito.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.