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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('genefu_2.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing genefu ───────────────────────────────────────────────────────────
✔ Package installed successfully
── genefu session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpHVs0KW/filea34e733f1111d/genefu
→ BiocVersion: 3.24
→ Package: genefu
→ PackageVersion: 2.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/genefu.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpHVs0KW/filea34e733f1111d/genefu
→ installDir: /tmp/RtmpHVs0KW/filea34e71cb16f30
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on genefu ─────────────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
VariantAnnotation, Survival, RNASeq, ImmunoOncology
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 (42%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of genefu...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/boxplotplus2.R (line 62, column 17)
    • ...
    • R/subtype.cluster.predict.R (line 125, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bimod.R (line 83, column 107)
    • ...
    • write.m.file.R (line 44, column 31)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/claudinLow.R (line 110, column 5)
    • print() in R/claudinLow.R (line 123, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/tbrm.R (line 45, column 6)
    • ...
    • R/tbrm.R (line 52, column 11)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/oncotypedx.R (line 109, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/genefu.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 20
functions greater than 50 lines.
  The longest 5 functions are:
    • subtype.cluster.predict() (R/subtype.cluster.predict.R): 241 lines
    • ...
    • intrinsic.cluster() (R/intrinsic.cluster.R): 146 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/mod1.Rd
    • ...
    • man/sigOvcYoshihara.Rd
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • collapseIDs.Rd
  • ...
  • readArray.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; 896 lines (13%) are > 80 characters long.
  First few lines:
    • R/bimod.R#L13 #' @param x Matrix containing the gene(s ...
    • ...
    • vignettes/genefu.Rmd#L815 - Doan, T.B. et al., 2014. Breast cancer ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1870 lines (27%) contain tabs.
  First few lines:
    • R/boxplotplus2.R#L53 y <- data.frame(t(x)) ...
    • ...
    • R/write.m.file.R#L46 invisible(res) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 522 lines (8%) are
not.
  First few lines:
    • R/bimod.R#L87 #How many Gaussians? ...
    • ...
    • vignettes/genefu.Rmd#L783 size="footnotesize",caption="Corr ...
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 | ⚠ 1 WARNINGS | ℹ 18 NOTES
ℹ See the genefu.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.