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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GOexpress_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GOexpress ────────────────────────────────────────────────────────
✔ Package installed successfully
── GOexpress session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2vi4Y0/fileaa8516b08c99b/GOexpress
→ BiocVersion: 3.24
→ Package: GOexpress
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GOexpress.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp2vi4Y0/fileaa8516b08c99b/GOexpress
→ installDir: /tmp/Rtmp2vi4Y0/fileaa8516c126bc8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GOexpress ──────────────────────────────────────────────
* 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 3.4 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/Rtmp2vi4Y0/fileaa8516b08c99b/GOexpress/man/expression_plot_symbol.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp2vi4Y0/fileaa8516b08c99b/GOexpress/man/heatmap_GO.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp2vi4Y0/fileaa8516b08c99b/GOexpress/man/hist_scores.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp2vi4Y0/fileaa8516b08c99b/GOexpress/man/list_genes.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp2vi4Y0/fileaa8516b08c99b/GOexpress/man/quantiles_scores.Rd'
* 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 (18%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • GOexpress-UsersGuide.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GOexpress-UsersGuide.Rnw
* Checking package installation calls in R code...
* Checking for library/require of GOexpress...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/toolkit.R (line 86, column 9)
    • ...
    • R/toolkit.R (line 231, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • post_analysis.R (line 341, column 9)
    • ...
    • toolkit.R (line 258, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/analysis.R (line 57, column 17)
    • ...
    • print() in R/toolkit.R (line 40, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/post_analysis.R (line 725, column 20)
    • ...
    • R/toolkit.R (line 213, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/post_analysis.R (line 198, column 17)
    • R/post_analysis.R (line 530, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • analysis.R (line 8, column 21)
    • ...
    • post_analysis.R (line 1072, column 24)
* 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:
    • GO_analyse() (R/analysis.R): 640 lines
    • ...
    • pValue_GO() (R/post_analysis.R): 135 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/AlvMac_allgenes.Rd
    • ...
    • man/prefix2dataset.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • pValue_GO.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:
    • GO_analyse.Rd
    • pValue_GO.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • GO_analyse.Rd
    • pValue_GO.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; 1 lines (0%) are > 80 characters long.
  First few lines:
    • vignettes/GOexpress-UsersGuide.Rnw#L103 Instructions to install the
    package are ...
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 | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the GOexpress.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.