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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('recoup_1.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing recoup ───────────────────────────────────────────────────────────
✔ Package installed successfully
── recoup session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp6wuO4K/file10de6c106c2082/recoup
→ BiocVersion: 3.24
→ Package: recoup
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/recoup.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp6wuO4K/file10de6c106c2082/recoup
→ installDir: /tmp/Rtmp6wuO4K/file10de6c59201e31
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on recoup ─────────────────────────────────────────────────
* 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 4.0.0 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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (54%).
* 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...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install() in R/annotation.R (line 1552, column 26)
* Checking for library/require of recoup...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/annotation.R (line 2901, column 13)
    • ...
    • print() in R/util.R (line 517, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotation.R (line 2363, column 19)
    • ...
    • R/ranges.R (line 377, column 8)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/annotation.R (line 774, column 21)
    • ...
    • R/recoup.R (line 601, column 26)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/annotation.R (line 1341, column 9)
    • system() in R/annotation.R (line 1372, column 5)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Defunct() in R/coverage.R (line 23, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 16 times)
  • suppressWarnings() in R/annotation.R (line 1583, column 39)
  • ...
  • suppressWarnings() in R/util.R (line 644, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 62
functions greater than 50 lines.
  The longest 5 functions are:
    • recoup() (R/recoup.R): 992 lines
    • ...
    • lazyRangesListCoverage() (R/coverage.R): 382 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • buildAnnotationDatabase.Rd
  • coverageRnaRef.Rd
  • getAnnotation.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • buildAnnotationDatabase.Rd
    • recoup.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 multiples of 4 spaces for line indents; 41 lines (0%) are not.
  First few lines:
    • R/plot.R#L193 scale_x_continuous(breaks=b ...
    • ...
    • man/recoupPlot.Rd#L42 \code{ggsave} or the base graphics de ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the recoup.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.