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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DRIMSeq_1.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DRIMSeq ──────────────────────────────────────────────────────────
✔ Package installed successfully
── DRIMSeq session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpIcbT47/file85556323da6de/DRIMSeq
→ BiocVersion: 3.24
→ Package: DRIMSeq
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DRIMSeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpIcbT47/file85556323da6de/DRIMSeq
→ installDir: /tmp/RtmpIcbT47/file8555657da2994
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DRIMSeq ────────────────────────────────────────────────
* 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 3.4.0 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...
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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (54%).
* 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:
    • DRIMSeq.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DRIMSeq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/class_dmSQTLprecision.R (line 147, column 5)
    • ...
    • R/dmSQTL_filter.R (line 154, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • class_dmDSdata.R (line 172, column 14)
    • ...
    • dmSQTL_permutations.R (line 222, column 22)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/class_show_utils.R (line 14, column 3)
    • ...
    • print in R/class_show_utils.R (line 92, column 8)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/class_dmDSfit.R (line 375, column 13)
    • ...
    • R/dmSQTL_permutations.R (line 135, column 15)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • class_dmDSdata.R (line 173, column 30)
    • ...
    • dmSQTL_fit.R (line 105, column 23)
* 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 32
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.349() (R/class_dmDStest.R): 170 lines
    • ...
    • dmSQTL_permutations_per_gene() (R/dmSQTL_permutations.R): 139 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 76% of man
pages use at least one of these tags.
  Found in files:
    • dmDSdata-class.Rd
    • ...
    • plotPValues.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; 154 lines (2%) are > 80 characters long.
  First few lines:
    • R/class_dmSQTLdata.R#L506 #' @param plot_type Character specifying ...
    • ...
    • vignettes/DRIMSeq.Rnw#L648 When the sample size is large, we recomm ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3260 lines (35%) are
not.
  First few lines:
    • R/class_dmDSdata.R#L71 representation(counts = "MatrixList", ...
    • ...
    • vignettes/DRIMSeq.Rnw#L660 plot_type = "boxplot2") ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 13 NOTES
ℹ See the DRIMSeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.