##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DiffBind_3.23.2.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing DiffBind ─────────────────────────────────────────────────────────
✔ Package installed successfully
── DiffBind session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpNQLNpy/file8232955bc50a/DiffBind
→ BiocVersion: 3.24
→ Package: DiffBind
→ PackageVersion: 3.23.2
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DiffBind.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpNQLNpy/file8232955bc50a/DiffBind
→ installDir: /tmp/RtmpNQLNpy/file823292add1fbc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DiffBind ───────────────────────────────────────────────
* 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: ChipOnChip,
Coverage, ExperimentalDesign
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...
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 (41%).
* 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:
    • DiffBind.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • DiffBind.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DiffBind...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/core.R (line 115, column 20)
    • ...
    • R/utils.R (line 474, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • analyze_deseq2.R (line 157, column 38)
    • ...
    • utils.R (line 838, column 16)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • report.R (line 509, column 24)
    • report.R (line 633, column 22)
    • utils.R (line 221, column 21)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/plots.R (line 694, column 9)
    • print() in R/plots.R (line 756, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/analyze_deseq2.R (line 63, column 38)
    • ...
    • R/utils.R (line 769, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/normalize.R (line 411, column 12)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/analyze_deseq2.R (line 204, column 14)
    • ...
    • R/plotProfile.R (line 471, column 30)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/io.R (line 141, column 20)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • io.R (line 143, column 26)
    • io.R (line 152, column 24)
    • io.R (line 152, column 58)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 30 times)
  • suppressMessages() in R/analyze_deseq2.R (line 183, column 10)
  • ...
  • suppressWarnings() in R/utils.R (line 364, column 18)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 71
functions greater than 50 lines.
  The longest 5 functions are:
    • pv.counts() (R/counts.R): 488 lines
    • ...
    • pv.normalize() (R/normalize.R): 283 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/dba.contrast.Rd
  • ...
  • man/tamoxifen.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/dba.plotMA.Rd
    • ...
    • man/print.DBA.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • dba.save.Rd
  • DiffBind-globals.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 20% of man
pages use at least one of these tags.
  Found in files:
    • dba.blacklist.Rd
    • ...
    • dba.save.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • dba.blacklist.Rd
    • ...
    • dba.save.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; 746 lines (3%) are > 80 characters long.
  First few lines:
    • R/analyze_deseq2.R#L282 res$block <- pv.DESeq2(pv,pv$c ...
    • ...
    • vignettes/DiffBind.Rnw#L3370 Researchers who contributed ideas and/or ...
ℹ NOTE: Consider 4 spaces instead of tabs; 336 lines (1%) contain tabs.
  First few lines:
    • R/analyze_deseq2.R#L14 return(res) ...
    • ...
    • vignettes/DiffBind.Rnw#L1043 all MCF7 sample replicates.} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 9307 lines (40%) are
not.
  First few lines:
    • R/analyze_deseq2.R#L2 bSubControl=TRUE,b ...
    • ...
    • vignettes/DiffBind.Rnw#L2919 ...
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 22 NOTES
ℹ See the DiffBind.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.