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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SomaticSignatures_2.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SomaticSignatures ────────────────────────────────────────────────
✔ Package installed successfully
── SomaticSignatures session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmptMqt73/file138c5629102f0b/SomaticSignatures
→ BiocVersion: 3.24
→ Package: SomaticSignatures
→ PackageVersion: 2.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SomaticSignatures.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmptMqt73/file138c5629102f0b/SomaticSignatures
→ installDir: /tmp/RtmptMqt73/file138c564bd5535
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SomaticSignatures ──────────────────────────────────────
* 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 3.5.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Coverage,
MotifAnnotation, VariantAnnotation, DataImport
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (60%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
  • knitr
✖ ERROR: No 'VignetteEngine' specified in vignette.
  Add 'VignetteEngine' to the following files:
    • vignettes/SomaticSignatures-vignette.Rhtml
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • SomaticSignatures-vignette.Rhtml
* Checking package installation calls in R code...
* Checking for library/require of SomaticSignatures...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/kmers.R (line 14, column 15)
    • R/utils.R (line 2, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • correlate.R (line 54, column 14)
    • ...
    • signature-plots.R (line 165, column 29)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/classes.R (line 18, column 23)
    • ...
    • R/utils.R (line 3, column 12)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressMessages() in R/granges-utils.R (line 2, column 5)
  • ...
  • suppressMessages() in R/rainfall.R (line 22, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • mutationContext() (R/mutation-context.R): 52 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/kmers-data.Rd
    • man/sca-data.Rd
    • man/signatures21-data.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/SomaticSignatures-package.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • cluster-spetrum.Rd
    • ...
    • MutationalSignatures-class.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; 203 lines (6%) are > 80 characters long.
  First few lines:
    • R/cluster.R#L1 clusterSpectrum <- function(m, by = c("s ...
    • ...
    • vignettes/SomaticSignatures-vignette.Rhtml#L1276 <h2
    id="orgheadline22"><span class="sect ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 543 lines (16%) are
not.
  First few lines:
    • R/classes.R#L2 slots = c( ...
    • ...
    • vignettes/SomaticSignatures-vignette.Rhtml#L1265 edition, Feb. 2010. ...
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 ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 2 WARNINGS | ℹ 12 NOTES
ℹ See the SomaticSignatures.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.