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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('xcore_1.17.0.tar.gz','quit-with-status'=TRUE)"
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── Installing xcore ────────────────────────────────────────────────────────────
✔ Package installed successfully
── xcore session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpy8pCng/file15455c6db1c4ff/xcore
→ BiocVersion: 3.24
→ Package: xcore
→ PackageVersion: 1.17.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/xcore.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpy8pCng/file15455c6db1c4ff/xcore
→ installDir: /tmp/Rtmpy8pCng/file15455c41da7edb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on xcore ──────────────────────────────────────────────────
* 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 4.2 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
ChipOnChip
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...
* 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 (43%).
* 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:
    • xcore_vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of xcore...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 7 times)
  • suppressMessages() in R/processing.R (line 381, column 5)
  • ...
  • suppressMessages() in R/stats.R (line 440, column 43)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
  The longest 5 functions are:
    • modelGeneExpression() (R/stats.R): 127 lines
    • modelGeneExpression_ridge_regression_wraper() (R/stats.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/pipe.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • pipe.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • design2factor.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • design2factor.Rd
* Checking package NEWS...
! WARNING: news(package='xcore') failed with news file: xcore/NEWS.md:news()
failed to parse news file: xcore/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; 107 lines (6%) are > 80 characters long.
  First few lines:
    • R/processing.R#L24 #' \item{U}{matrix giving expression ...
    • ...
    • vignettes/xcore_vignette.Rmd#L204 backend, together with
    [`BiocParallel`]( ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • vignettes/xcore_vignette.Rmd#L35 You can install `xcore` package from Bio
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 374 lines (21%) are
not.
  First few lines:
    • R/processing.R#L56 design, ...
    • ...
    • vignettes/xcore_vignette.Rmd#L323 ext = 500 ...
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 | ⚠ 2 WARNINGS | ℹ 14 NOTES
ℹ See the xcore.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.