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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('dks_1.59.0.tar.gz','quit-with-status'=TRUE)"
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── Installing dks ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── dks session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJaVsgf/file837f0681605cc/dks
→ BiocVersion: 3.24
→ Package: dks
→ PackageVersion: 1.59.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/dks.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpJaVsgf/file837f0681605cc/dks
→ installDir: /tmp/RtmpJaVsgf/file837f01d49c8a8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on dks ────────────────────────────────────────────────────
* 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 2.8 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpJaVsgf/file837f0681605cc/dks/man/dksdata.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: ATACSeq,
DNASeq
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...
! 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:
    • dks.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/dks.Rnw
* Checking package installation calls in R code...
* Checking for library/require of dks...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dks.R (line 67, column 12)
    • ...
    • dks.R (line 137, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/dks.R (line 99, column 12)
    • cat() in R/dks.R (line 101, column 12)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/dksdata.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; 99 lines (17%) are > 80 characters long.
  First few lines:
    • R/dks.R#L3 ## Calculate the posterior probability a ...
    • ...
    • vignettes/dks.Rnw#L168 \bibitem{leek:2011aa} Leek J.T. and Stor ...
ℹ NOTE: Consider 4 spaces instead of tabs; 10 lines (2%) contain tabs.
  First few lines:
    • man/cred.set.Rd#L15 \item{level}{The level of the credible ...
    • ...
    • vignettes/dks.Rnw#L156 points(0,0,col="blue",cex=1,pch=19) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 219 lines (37%) are
not.
  First few lines:
    • R/dks.R#L7 p <- pmax(pmin(p,1-1e-11),1e-11) ...
    • ...
    • vignettes/dks.Rnw#L162 \caption{A plot of the 80\% credible s ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 12 NOTES
ℹ See the dks.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.