Back to BiocCheck report for a small subset of BioC 3.19 packages

This page was generated on 2024-06-24 11:15:01 -0400 (Mon, 24 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
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 112/119HostnameOS / ArchBUILDBIOCCHECK
tximport 1.33.0  (landing page)
Michael Love
Snapshot Date: 2024-06-24 10:00:01 -0400 (Mon, 24 Jun 2024)
git_url: https://git.bioconductor.org/packages/tximport
git_branch: devel
git_last_commit: ec99ce8
git_last_commit_date: 2024-04-30 10:48:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    ERROR  

BIOCCHECK results for tximport on nebbiolo1


To the developers/maintainers of the tximport 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: tximport
Version: 1.33.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('tximport_1.33.0.tar.gz')"
StartedAt: 2024-06-24 10:43:26 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 10:43:41 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 14.6 seconds
RetCode: None
Status:   ERROR  
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('tximport_1.33.0.tar.gz')"
###
##############################################################################
##############################################################################


─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: tximport
─ PackageVersion: 1.33.0
─ sourceDir: /tmp/RtmpnATeC7/file28b1c71db639c0/tximport
─ installDir: /tmp/RtmpnATeC7/file28b1c7659074a
─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/tximport.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...
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * NOTE: The Description field in the DESCRIPTION is made up of less
      than 3 sentences. Provide a more detailed description of the
      package.
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    * WARNING: No Bioconductor dependencies detected. Note that some
      infrastructure packages may not have Bioconductor dependencies.
      For more information, reach out to the Bioconductor community
      and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of tximport...
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 6 functions greater than 50 lines.
* Checking man page documentation...
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
* 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; 112 lines (6%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 651 lines
      (32%) 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 is in the Support Site Watched Tags.

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

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