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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('vulcan_1.35.0.tar.gz','quit-with-status'=TRUE)"
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── Installing vulcan ───────────────────────────────────────────────────────────
✔ Package installed successfully
── vulcan session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpzHCYvy/file1532293b6d9868/vulcan
→ BiocVersion: 3.24
→ Package: vulcan
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/vulcan.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpzHCYvy/file1532293b6d9868/vulcan
→ installDir: /tmp/RtmpzHCYvy/file1532295f46278
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on vulcan ─────────────────────────────────────────────────
* 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 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Epigenetics, Coverage, Normalization, ChIPchip, ATACSeq, DNaseSeq, RIPSeq,
MethylSeq, CellBiology, BiomedicalInformatics, FunctionalGenomics,
DifferentialMethylation, DifferentialPeakCalling, FunctionalPrediction,
GeneRegulation, HistoneModification, PeakDetection, MultipleComparison,
ReportWriting
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 (47%).
* 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:
    • vulcan.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • vulcan.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/vulcan.Rnw
* Checking package installation calls in R code...
* Checking for library/require of vulcan...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/gsea.R (line 174, column 18)
    • ...
    • R/rea.R (line 87, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • generic.R (line 102, column 18)
    • ...
    • vulcan.R (line 428, column 22)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/generic.R (line 102, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/generic.R (line 184, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • F in R/vulcan.R (line 432, column 68)
    • F in R/vulcan.R (line 432, column 122)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • gsea.R (line 104, column 28)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/vulcan.R (line 415, column 5)
  • set.seed() in R/vulcan.R (line 514, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/gsea.R (line 528, column 10)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
  The longest 5 functions are:
    • plot_gsea() (R/gsea.R): 186 lines
    • ...
    • dist_calc() (R/vulcan.R): 83 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • vulcan.normalize.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • vulcan.normalize.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • vulcan.normalize.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; 3 lines (0%) are > 80 characters long.
  First few lines:
    • R/vulcan.R#L432 tmp <- cbind(unlist(lapply(tmp, func ...
    • vulcan/NAMESPACE#L39 importFrom('DESeq2','DESeqDataSetFromMat ...
    • vignettes/vulcan.Rnw#L16 \affil[1]{Department of Pharmacy and Bio ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2 lines (0%) are not.
  First few lines:
    • R/vulcan.R#L420 colData=co ...
    • R/vulcan.R#L421 design=~sa ...
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 | ⚠ 4 WARNINGS | ℹ 19 NOTES
ℹ See the vulcan.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.