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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('DEXSeq_1.58.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DEXSeq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── DEXSeq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpeToxAs/file76ae15e68b6fb/DEXSeq
→ BiocVersion: 3.23
→ Package: DEXSeq
→ PackageVersion: 1.58.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/DEXSeq.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpeToxAs/file76ae15e68b6fb/DEXSeq
→ installDir: /tmp/RtmpeToxAs/file76ae15f62411e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DEXSeq ─────────────────────────────────────────────────
* 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...
* 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,
Normalization
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 that Package field matches directory/tarball name...
* Checking for Version: field...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (76%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • DEXSeq.Rmd
* Checking package installation calls in R code...
* Checking for library/require of DEXSeq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/classes.R (line 285, column 15)
    • ...
    • R/visualization.R (line 199, column 33)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • classes.R (line 339, column 62)
    • ...
    • visualization.R (line 281, column 29)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/coef_handling.R (line 163, column 17)
    • ...
    • cat() in R/methods.R (line 224, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/classes.R (line 89, column 26)
    • ...
    • R/perGeneQValue.R (line 80, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/coef_handling.R (line 118, column 29)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/visualization.R (line 117, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • plotDEXSeq() (R/visualization.R): 255 lines
    • ...
    • estimateDispersions.DEXSeqDataSet() (R/methods.R): 100 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/DEXSeq-defunct.Rd
    • ...
    • man/plotMA.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • DEXSeq.Rd
    • ...
    • plotMA.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 29% of man
pages use at least one of these tags.
  Found in files:
    • DEXSeq.Rd
    • ...
    • plotMA.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • DEXSeq.Rd
    • ...
    • plotMA.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: Add content to the empty file R/deprecatedFunctions.R
ℹ NOTE: Consider shorter lines; 381 lines (14%) are > 80 characters long.
  First few lines:
    • R/classes.R#L5 DEXSeqDataSet <- function( countData, sa ...
    • ...
    • vignettes/DEXSeq.Rmd#L675 The session information records the vers ...
ℹ NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain tabs.
  First few lines:
    • R/htmlReports.R#L66 ...
    • ...
    • vignettes/DEXSeq.Rmd#L352 reducedModel = formulaReducedModel, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 856 lines (33%) are
not.
  First few lines:
    • R/classes.R#L9 stop( "Unexpected input: the param ...
    • ...
    • vignettes/DEXSeq.Rmd#L635 IRanges(start=3872658, end=3875302) ) ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 19 NOTES
ℹ See the DEXSeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.