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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('PWMEnrich_4.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing PWMEnrich ────────────────────────────────────────────────────────
✔ Package installed successfully
── PWMEnrich session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmptjen1p/file1045925dedd269/PWMEnrich
→ BiocVersion: 3.24
→ Package: PWMEnrich
→ PackageVersion: 4.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/PWMEnrich.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmptjen1p/file1045925dedd269/PWMEnrich
→ installDir: /tmp/Rtmptjen1p/file104592219b3131
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on PWMEnrich ──────────────────────────────────────────────
* 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: Sequencing,
Alignment, MotifDiscovery, 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 (50%).
* 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:
    • PWMEnrich.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • PWMEnrich.Rnw
* Checking package installation calls in R code...
* Checking for library/require of PWMEnrich...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/background.R (line 134, column 19)
    • ...
    • R/similarity.R (line 70, column 33)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • background.R (line 113, column 37)
    • ...
    • similarity.R (line 70, column 40)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/background.R (line 101, column 9)
    • ...
    • cat() in R/pwm.R (line 1086, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/background.R (line 6, column 19)
    • ...
    • R/similarity.R (line 157, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/background.R (line 642, column 30)
    • ...
    • R/readData.R (line 130, column 30)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/background.R (line 678, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/misc.R (line 4, column 35)
    • T in R/misc.R (line 10, column 31)
* 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 19
functions greater than 50 lines.
  The longest 5 functions are:
    • makePWMLognBackground() (R/background.R): 173 lines
    • ...
    • logNormPval() (R/pwm.R): 101 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/affinitySequenceSet.Rd
    • ...
    • man/useBigMemoryPWMEnrich.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • as.data.frame-MotifEnrichmentReport-method.Rd
    • ...
    • useBigMemoryPWMEnrich.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 13% of man
pages use at least one of these tags.
  Found in files:
    • getBackgroundFrequencies.Rd
    • ...
    • useBigMemoryPWMEnrich.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getBackgroundFrequencies.Rd
    • ...
    • useBigMemoryPWMEnrich.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; 613 lines (12%) are > 80 characters long.
  First few lines:
    • R/AllDataClasses.R#L9 #' \item{\code{id}:}{a systematic ID ...
    • ...
    • vignettes/PWMEnrich.Rnw#L312 The resulting \Robject{bg.custom} object ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2468 lines (47%) contain tabs.
  First few lines:
    • R/AllDataClasses.R#L17 representation = representation( ...
    • ...
    • vignettes/PWMEnrich.Rnw#L307 bg.source="20 promoters split into 100b ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 186 lines (4%) are
not.
  First few lines:
    • R/plot.R#L206 if (inherits(pwm, "pwm")){ ...
    • ...
    • vignettes/PWMEnrich.Rnw#L270 ...
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 | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the PWMEnrich.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.