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 27/92HostnameOS / ArchBIOCCHECK
cytolib 2.13.1  (landing page)
Mike Jiang
Snapshot Date: 2023-10-24 10:00:01 -0400 (Tue, 24 Oct 2023)
git_url: https://git.bioconductor.org/packages/cytolib
git_branch: devel
git_last_commit: 1e773e3
git_last_commit_date: 2023-07-10 14:51:37 -0400 (Mon, 10 Jul 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  ERROR  

BIOCCHECK results for cytolib on nebbiolo2


To the developers/maintainers of the cytolib 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: cytolib
Version: 2.13.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('cytolib_2.13.1.tar.gz')"
StartedAt: 2023-10-24 10:46:11 -0400 (Tue, 24 Oct 2023)
EndedAt: 2023-10-24 10:49:13 -0400 (Tue, 24 Oct 2023)
EllapsedTime: 181.2 seconds
RetCode: None
Status:   ERROR  
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('cytolib_2.13.1.tar.gz')"
###
##############################################################################
##############################################################################


─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: cytolib
─ PackageVersion: 2.13.1
─ sourceDir: /tmp/RtmpSW25VN/file38a5241222ae7e/cytolib
─ installDir: /tmp/RtmpSW25VN/file38a52463f2d36e
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/cytolib.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...
    * NOTE: Update R version dependency from 3.4 to 4.3.0.
* 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...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* 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 recommeded fields in DESCRIPTION...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * WARNING: Evaluate more vignette chunks.
        1 out of 2 code chunks = 50% unevaluated
        1 non-exec code chunk(s) (e.g., '```r')
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking package installation calls in R code...
* Checking for library/require of cytolib...
* Checking coding practice...
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
    * WARNING: Empty or missing \value sections found in man pages.
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples.
* Checking package NEWS...
    * NOTE: Consider adding a NEWS file, so your package news will be
      included in Bioconductor release announcements.
* Checking unit tests...
    * 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...
    * NOTE: Consider shorter lines; 9 lines (10%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 13 lines
      (14%) 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...
    * ERROR: Maintainer must register at the support site; visit
      https://support.bioconductor.org/accounts/signup/

─ BiocCheck results ──
4 ERRORS | 3 WARNINGS | 9 NOTES

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