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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DeMAND_1.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DeMAND ───────────────────────────────────────────────────────────
✔ Package installed successfully
── DeMAND session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpBcTmyd/file80c342140e455/DeMAND
→ BiocVersion: 3.24
→ Package: DeMAND
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DeMAND.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpBcTmyd/file80c342140e455/DeMAND
→ installDir: /tmp/RtmpBcTmyd/file80c3419558bd7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DeMAND ─────────────────────────────────────────────────
* 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 2.14.0 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...
* 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...
ℹ NOTE: License 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* 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:
    • DeMAND.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • DeMAND.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DeMAND...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/KLD2D.r (line 11, column 3)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/pareto.R (line 142, column 19)
    • R/pareto.R (line 247, column 13)
    • R/runDeMAND_ys.R (line 119, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • integratePvalues.r (line 26, column 48)
    • ...
    • runDeMAND_ys.R (line 131, column 32)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/pareto.R (line 127, column 7)
    • print() in R/printDeMAND.R (line 21, column 30)
    • print() in R/printDeMAND.R (line 24, column 30)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/demandClass.R (line 34, column 26)
    • ...
    • R/pareto.R (line 247, column 11)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 6 times:
    • F in R/integratePvalues.r (line 52, column 57)
    • ...
    • F in R/runDeMAND_ys.R (line 130, column 66)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/runDeMAND.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/pareto.R (line 166, column 8)
* 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:
    • runDeMAND() (R/runDeMAND_ys.R): 117 lines
    • KLD2D() (R/KLD2D.r): 55 lines
    • integratePvalues() (R/integratePvalues.r): 53 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/bcellAnno.Rd
    • ...
    • man/controlIndex.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 105 lines (11%) are > 80 characters long.
  First few lines:
    • R/demandClass.R#L8 #' \item{\code{anno}:}{Matrix conta ...
    • ...
    • vignettes/DeMAND.Rnw#L94 \bibitem{Lefebvre2010} Lefebvre, C. et a ...
ℹ NOTE: Consider 4 spaces instead of tabs; 33 lines (4%) contain tabs.
  First few lines:
    • R/pareto.R#L5 # dpareto Probability density ...
    • ...
    • R/pareto.R#L359 # with period, hiding them in workspa ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 336 lines (36%) are
not.
  First few lines:
    • R/integratePvalues.r#L2 #' This function integrates the p-valu ...
    • ...
    • man/runDeMAND.Rd#L6 keepLeaves=FALSE, alpha=0.05) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | ℹ 18 NOTES
ℹ See the DeMAND.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.