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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MotifDb_1.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MotifDb ──────────────────────────────────────────────────────────
✔ Package installed successfully
── MotifDb session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmptJLoEl/filee092a131bda72/MotifDb
→ BiocVersion: 3.24
→ Package: MotifDb
→ PackageVersion: 1.55.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MotifDb.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmptJLoEl/filee092a131bda72/MotifDb
→ installDir: /tmp/RtmptJLoEl/filee092a2da28462
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MotifDb ────────────────────────────────────────────────
* 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: Transcription,
Sequencing, Alignment, MultipleSequenceAlignment, SequenceMatching, 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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (75%).
* 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:
  • rmarkdown
  • formatR
  • markdown
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/MotifDb.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MotifDb...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/MotifList-class.R (line 26, column 14)
    • ...
    • R/MotifList-class.R (line 314, column 36)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • MotifList-class.R (line 166, column 15)
    • ...
    • MotifList-class.R (line 396, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/zzz.R (line 25, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/MotifList-class.R (line 18, column 9)
    • ...
    • R/zzz.R (line 18, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/zzz.R (line 37, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.452() (R/MotifList-class.R): 65 lines
    • _anonymous_.244() (R/MotifList-class.R): 55 lines
    • matrixToMemeText() (R/MotifList-class.R): 52 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/MotifDb.Rd
See system.file("LICENSE", package="MotifDb") for use restrictions.
* 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; 119 lines (9%) are > 80 characters long.
  First few lines:
    • R/MotifList-class.R#L1 setGeneric('query', signature='object', ...
    • ...
    • vignettes/MotifDb.Rmd#L104 DNAse footprinting, epigenetic markers, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 447 lines (33%) are
not.
  First few lines:
    • R/MotifList-class.R#L5 function(object, tbl.withMoti ...
    • ...
    • vignettes/MotifDb.Rmd#L41 * Cooperativity with other DNA-binding ...
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 | ⚠ 1 WARNINGS | ℹ 14 NOTES
ℹ See the MotifDb.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.