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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GPA_1.25.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GPA ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── GPA session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4fBJAC/fileac1ec33c69a41/GPA
→ BiocVersion: 3.24
→ Package: GPA
→ PackageVersion: 1.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GPA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp4fBJAC/fileac1ec33c69a41/GPA
→ installDir: /tmp/Rtmp4fBJAC/fileac1ec78cdbcb7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GPA ────────────────────────────────────────────────────
* 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 4.0.0 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • GPA-example.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • GPA-example.Rnw
* Checking package installation calls in R code...
* Checking for library/require of GPA...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • shinyGPA.R (line 416, column 39)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/aTest.R (line 115, column 9)
    • ...
    • print() in R/shinyGPA.R (line 428, column 8)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/shinyGPA.R (line 252, column 15)
* 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 9
functions greater than 50 lines.
  The longest 5 functions are:
    • shinyGPA() (R/shinyGPA.R): 434 lines
    • ...
    • aTest() (R/aTest.R): 167 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
  Found in files:
    • GPA-package.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • GPA-package.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; 185 lines (6%) are > 80 characters long.
  First few lines:
    • R/assoc.R#L10 stop( "Invalid value for 'fdrControl' ...
    • ...
    • vignettes/GPA-example.Rnw#L291 ``Accurately assessing the risk of schiz
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 826 lines (28%) contain tabs.
  First few lines:
    • R/AllClasses.R#L7 setting="list", ...
    • ...
    • man/pTest.Rd#L17 For example, setting it to 1000 means ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 387 lines (13%) are
not.
  First few lines:
    • R/AllGenerics.R#L4 "get_fit", ...
    • ...
    • vignettes/GPA-example.Rnw#L280 \textit{PLOS One}, 13(1): e0190949. ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | ℹ 13 NOTES
ℹ See the GPA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.