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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ggbio_1.60.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ggbio ────────────────────────────────────────────────────────────
✔ Package installed successfully
── ggbio session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNX9Zvn/file15b21d76086d43/ggbio
→ BiocVersion: 3.23
→ Package: ggbio
→ PackageVersion: 1.60.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ggbio.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpNX9Zvn/file15b21d76086d43/ggbio
→ installDir: /tmp/RtmpNX9Zvn/file15b21d6ce2307c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ggbio ──────────────────────────────────────────────────
* 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...
* 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 that Package field matches directory/tarball name...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (61%).
* 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:
    • ggbio.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ggbio.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ggbio...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/autoplot-method.R (line 1103, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/autoplot-method.R (line 1411, column 13)
    • ...
    • R/theme.R (line 141, column 36)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • autoplot-method.R (line 1013, column 19)
    • ...
    • Tracks-class.R (line 755, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/ideogram.R (line 144, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/autoplot-method.R (line 773, column 40)
    • ...
    • R/geom_alignment-method.R (line 73, column 27)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/autoplot-method.R (line 723, column 39)
    • ...
    • R/plotSpliceSum-method.R (line 38, column 24)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/stat_gene-method.R (line 4, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/GGbio-class.R (line 328, column 5)
  • ...
  • suppressWarnings() in R/utils.R (line 54, column 15)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 49
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.4() (R/layout_circle-method.R): 348 lines
    • ...
    • _anonymous_.1332() (R/autoplot-method.R): 200 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/ggsave.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • ggsave.Rd
    • ...
    • stat_mismatch-method.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
  Found in files:
    • autoplot-method.Rd
    • ...
    • stat_gene-method.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • autoplot-method.Rd
    • ...
    • stat_gene-method.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 shorter lines; 385 lines (3%) are > 80 characters long.
  First few lines:
    • R/autoplot-method.R#L31 ...
    • ...
    • man/tracks.Rd#L467 tracks(time1 = p1, time2 = p2, xlab = "t ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • man/tracks.Rd#L252 \code{\linkS4class{GRanges}} object. Th ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4297 lines (30%) are
not.
  First few lines:
    • R/AllClasses.R#L17 c("GRanges", "AnnotationFi ...
    • ...
    • man/tracks.Rd#L443 tracks(p1, p2) + theme_tracks_sunset() ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the ggbio.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.