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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RTCGAToolbox_2.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RTCGAToolbox ─────────────────────────────────────────────────────
✔ Package installed successfully
── RTCGAToolbox session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUYunx2/file1269dd5b8ab5e5/RTCGAToolbox
→ BiocVersion: 3.24
→ Package: RTCGAToolbox
→ PackageVersion: 2.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RTCGAToolbox.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUYunx2/file1269dd5b8ab5e5/RTCGAToolbox
→ installDir: /tmp/RtmpUYunx2/file1269dd661e1b02
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RTCGAToolbox ───────────────────────────────────────────
* 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 4.3.0 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • RTCGAToolbox-vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RTCGAToolbox...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getFirehoseData.R (line 27, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • getFirehoseData.R (line 7, column 17)
    • ...
    • getFirehoseData.R (line 617, column 31)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/RTCGAToolbox-Class.R (line 292, column 3)
    • print() in R/RTCGAToolbox-Class.R (line 317, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getFirehoseData.R (line 5, column 11)
    • ...
    • R/getMutationRate.R (line 25, column 27)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/getBroadSubtypes.R (line 40, column 17)
    • ...
    • R/RTCGAToolbox-Class.R (line 316, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/utils.R (line 183, column 10)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
  The longest 5 functions are:
    • getFirehoseData() (R/getFirehoseData.R): 549 lines
    • ...
    • makeSummarizedExperimentFromGISTIC()
    (R/makeSummarizedExperimentFromGISTIC.R): 56 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/FirehoseData-class.Rd
    • man/FirehoseGISTIC-class.Rd
    • man/hg19.ucsc.gene.locations.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • selectType.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:
    • getFirehoseData.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getFirehoseData.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; 128 lines (5%) are > 80 characters long.
  First few lines:
    • R/getFirehoseAnalyzeDates.R#L3 #' `getFirehoseAnalyzeDates` returns the
    ...
    • ...
    • vignettes/RTCGAToolbox-vignette.Rmd#L26 - family: Mermel, C. H. and
    Schumacher ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 439 lines (16%) are
not.
  First few lines:
    • R/getFirehoseData.R#L4 #Get selected type only ...
    • ...
    • R/utils.R#L275 build <- .validateNCBI(build) ...
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 17 NOTES
ℹ See the RTCGAToolbox.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.