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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('TCGAbiolinks_2.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing TCGAbiolinks ─────────────────────────────────────────────────────
✔ Package installed successfully
── TCGAbiolinks session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks
→ BiocVersion: 3.24
→ Package: TCGAbiolinks
→ PackageVersion: 2.41.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/TCGAbiolinks.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks
→ installDir: /tmp/RtmpAVn4Qs/file2e4b513439fa46
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TCGAbiolinks ───────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.1.0 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (17%).
* 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:
    • analysis.Rmd
    • ...
    • subtypes.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/classifiers.Rmd
    • ...
    • vignettes/stemness_score.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/analysis.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/casestudy.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/classifiers.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/clinical.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/download_prepare.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/extension.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/index.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/mutation.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/query.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/stemness_score.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpAVn4Qs/file2e4b51208d4ef3/TCGAbiolinks/vignettes/subtypes.Rmd
* Checking package installation calls in R code...
* Checking for library/require of TCGAbiolinks...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/classifiers.R (line 103, column 18)
    • ...
    • R/visualize.R (line 1101, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • analyze.R (line 103, column 33)
    • ...
    • visualize.R (line 1593, column 42)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/analyze.R (line 450, column 21)
    • ...
    • print() in R/visualize.R (line 1083, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/analyze.R (line 130, column 15)
    • ...
    • R/visualize.R (line 1556, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/analyze.R (line 620, column 34)
    • ...
    • R/visualize.R (line 1420, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/api.R (line 144, column 27)
    • ...
    • R/visualize.R (line 702, column 25)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 15 times:
    • T in R/analyze.R (line 598, column 63)
    • ...
    • T in R/query.R (line 527, column 70)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/download.R (line 122, column 21)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/mutation.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/prepare.R (line 549, column 28)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12 times)
  • suppressWarnings() in R/methylation.R (line 150, column 5)
  • ...
  • suppressMessages() in R/visualize.R (line 985, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 50
functions greater than 50 lines.
  The longest 5 functions are:
    • TCGAvisualize_oncoprint() (R/visualize.R): 481 lines
    • ...
    • GDCquery_clinic() (R/clinical.R): 303 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/colDataPrepare.Rd
    • ...
    • man/splitAPICall.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • GDCdownload.Rd
    • ...
    • UseRaw_afterFilter.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 29% of man
pages use at least one of these tags.
  Found in files:
    • GDCdownload.Rd
    • ...
    • UseRaw_afterFilter.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • GDCdownload.Rd
    • ...
    • UseRaw_afterFilter.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test-prepare-download.R
test-query-clinical.R test-query.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 1367 lines (9%) are > 80 characters long.
  First few lines:
    • R/analyze.R#L24 stop("ConsensusClusterPlus is ne ...
    • ...
    • vignettes/subtypes.Rmd#L104 | UVM | http://www.cell.com/cancer-cell/ ...
ℹ NOTE: Consider 4 spaces instead of tabs; 156 lines (1%) contain tabs.
  First few lines:
    • vignettes/analysis.Rmd#L368 * **main** main title of the plot ...
    • ...
    • vignettes/subtypes.Rmd#L104 | UVM | http://www.cell.com/cancer-cell/ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 506 lines (3%) are
not.
  First few lines:
    • R/analyze.R#L140 xaxt = "n", ...
    • ...
    • vignettes/stemness_score.Rmd#L81 colname.score = "MESO_PCBC_stem_score"
    ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 23 NOTES
ℹ See the TCGAbiolinks.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.