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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DExMA_1.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DExMA ────────────────────────────────────────────────────────────
✔ Package installed successfully
── DExMA session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpx5o2GD/file81f75103f87ac/DExMA
→ BiocVersion: 3.24
→ Package: DExMA
→ PackageVersion: 1.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DExMA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpx5o2GD/file81f75103f87ac/DExMA
→ installDir: /tmp/Rtmpx5o2GD/file81f754055cfad
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DExMA ──────────────────────────────────────────────────
* 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 4.1 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 (35%).
* 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:
    • DExMA.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • DExMA.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DExMA...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/calculateES.R (line 100, column 13)
    • ...
    • print() in R/pvalueIndAnalysis.R (line 149, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/batchRemove.R (line 65, column 12)
    • ...
    • R/pvalueIndAnalysis.R (line 136, column 13)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • dataLog.R (line 46, column 40)
    • dataLog.R (line 50, column 35)
    • dataLog.R (line 63, column 35)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • makeHeatmap() (R/makeHeatmap.R): 63 lines
    • ...
    • pvalueIndAnalysis() (R/pvalueIndAnalysis.R): 51 lines
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • downloadGEOData.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • downloadGEOData.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • downloadGEOData.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; 97 lines (3%) are > 80 characters long.
  First few lines:
    • R/allSameID.R#L139 agregMatrix <- aggregate(annotMatrix ...
    • ...
    • vignettes/DExMA.Rnw#L520 Similar to the calculation of effects si ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 102 lines (3%) are
not.
  First few lines:
    • R/makeHeatmap.R#L116 scaling<-match.arg(scaling) ...
    • ...
    • R/makeHeatmap.R#L289 return(exp.ALL) ...
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 14 NOTES
ℹ See the DExMA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.