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###
### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GDCRNATools_1.33.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing GDCRNATools ──────────────────────────────────────────────────────
✔ Package installed successfully
── GDCRNATools session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2ToW40/filea1cee2d871c8d/GDCRNATools
→ BiocVersion: 3.24
→ Package: GDCRNATools
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GDCRNATools.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp2ToW40/filea1cee2d871c8d/GDCRNATools
→ installDir: /tmp/Rtmp2ToW40/filea1cee2314c06
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GDCRNATools ────────────────────────────────────────────
* 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 3.5.0 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: ShinyApps
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* 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 (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...
! WARNING: Evaluate more vignette chunks.
ℹ 1 out of 1 code chunks = 100% unevaluated
ℹ 
* Checking package installation calls in R code...
* Checking for library/require of GDCRNATools...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • gdcClinical.R (line 327, column 31)
    • gdcSurvivalAnalysis.R (line 87, column 43)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/gdcVoomNormalization.R (line 36, column 9)
    • cat() in R/gdcVoomNormalization.R (line 37, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/gdcCEAnalysis.R (line 122, column 15)
    • ...
    • R/gdcVoomNormalization.R (line 28, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/gdcClinical.R (line 61, column 26)
    • ...
    • R/gdcRNAMerge.R (line 99, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • T in R/gdcRNAMerge.R (line 40, column 37)
    • ...
    • F in R/gdcRNAMerge.R (line 43, column 36)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/gdcRNADownload.R (line 145, column 13)
    • system() in R/gdcRNADownload.R (line 152, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/gdcParseMetadata.R (line 93, column 25)
  • suppressWarnings() in R/gdcParseMetadata.R (line 96, column 22)
  • suppressWarnings() in R/gdcParseMetadata.R (line 99, column 31)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
  The longest 5 functions are:
    • gdcClinicalMerge() (R/gdcClinical.R): 204 lines
    • ...
    • gdcKMPlot() (R/gdcKMPlot.R): 91 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/DEGAll.Rd
    • ...
    • man/rnaCounts.Rd


##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
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:
    • gdcClinicalDownload.Rd
    • ...
    • shinyPathview.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • gdcClinicalDownload.Rd
    • ...
    • shinyPathview.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; 18 lines (1%) are > 80 characters long.
  First few lines:
    • R/gdcClinical.R#L256 cleantable<- rbind(line1 ...
    • ...
    • vignettes/index.Rmd#L49 A simply manual of `GDCRNATools` is avai ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/gdcRNADownload.R#L187 workflow.type <- 'STAR - Counts' ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 24 lines (1%) are not.
  First few lines:
    • R/gdcClinical.R#L293 line8 ...
    • ...
    • R/gdcRNAMerge.R#L76 paste('Number of genes: ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the GDCRNATools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.