Back to BiocCheck report for a small subset of BioC 3.18 packages

This page was generated on 2023-10-24 11:15:02 -0400 (Tue, 24 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4818
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 47/92HostnameOS / ArchBIOCCHECK
Gviz 1.47.0  (landing page)
Robert Ivanek
Snapshot Date: 2023-10-24 10:00:01 -0400 (Tue, 24 Oct 2023)
git_url: https://git.bioconductor.org/packages/Gviz
git_branch: devel
git_last_commit: ffb9430
git_last_commit_date: 2023-10-24 09:49:23 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  ERROR  

BIOCCHECK results for Gviz on nebbiolo2


To the developers/maintainers of the Gviz package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: Gviz
Version: 1.47.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Gviz_1.47.0.tar.gz')"
StartedAt: 2023-10-24 10:46:59 -0400 (Tue, 24 Oct 2023)
EndedAt: 2023-10-24 10:48:53 -0400 (Tue, 24 Oct 2023)
EllapsedTime: 113.7 seconds
RetCode: None
Status:   ERROR  
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Gviz_1.47.0.tar.gz')"
###
##############################################################################
##############################################################################


─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: Gviz
─ PackageVersion: 1.47.0
─ sourceDir: /tmp/Rtmp5NjAby/file38c81c27f9d4bf/Gviz
─ installDir: /tmp/Rtmp5NjAby/file38c81c7e0a256e
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/Gviz.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* 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...
* Checking package size...
    * ERROR: Package tarball exceeds the Bioconductor size requirement.
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Coverage, Alignment, DataImport
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of Gviz...
* Checking coding practice...
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
    * WARNING: Remove browser() statements (found 15 times)
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 19
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 39 functions greater than 50 lines.
* Checking man page documentation...
    * WARNING: Empty or missing \value sections found in man pages.
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 15% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 1969 lines (7%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 553 lines
      (2%) are not.
    See https://contributions.bioconductor.org/r-code.html
    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...
    * 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...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

─ BiocCheck results ──
1 ERRORS | 2 WARNINGS | 10 NOTES

See the Gviz.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.