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

This page was generated on 2024-06-28 11:15:01 -0400 (Fri, 28 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 6/119HostnameOS / ArchBUILDBIOCCHECK
AnnotationDbi 1.67.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-06-28 10:00:01 -0400 (Fri, 28 Jun 2024)
git_url: https://git.bioconductor.org/packages/AnnotationDbi
git_branch: devel
git_last_commit: f92007d
git_last_commit_date: 2024-04-30 10:16:08 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    ERROR  

BIOCCHECK results for AnnotationDbi on nebbiolo1


To the developers/maintainers of the AnnotationDbi 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: AnnotationDbi
Version: 1.67.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('AnnotationDbi_1.67.0.tar.gz')"
StartedAt: 2024-06-28 10:43:58 -0400 (Fri, 28 Jun 2024)
EndedAt: 2024-06-28 10:44:40 -0400 (Fri, 28 Jun 2024)
EllapsedTime: 41.9 seconds
RetCode: None
Status:   ERROR  
Warnings: 6

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('AnnotationDbi_1.67.0.tar.gz')"
###
##############################################################################
##############################################################################


─ BiocCheckVersion: 1.41.3
─ BiocVersion: 3.20
─ Package: AnnotationDbi
─ PackageVersion: 1.67.0
─ sourceDir: /tmp/RtmpKv9KwN/file3ac5ce5e28acb0/AnnotationDbi
─ installDir: /tmp/RtmpKv9KwN/file3ac5ce358fd4d8
─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/AnnotationDbi.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 2.7.0 to 4.4.0.
* 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...
    * NOTE: Consider adding these automatically suggested biocViews: GO
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...
    * 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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (50%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
* Checking package installation calls in R code...
* Checking for library/require of AnnotationDbi...
    * WARNING: Avoid the use of 'library' or 'require' in R code
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
    * WARNING: Avoid class membership checks with class() / is() and ==
      / !=; Use is(x, 'class') for S4 classes
    * WARNING: .Deprecated / .Defunct usage (found 2 times)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 15 functions greater than 50 lines.
* Checking man page documentation...
    * WARNING: Empty or missing \value sections found in man page(s).
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 8% 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; 280 lines (2%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 54 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 2521 lines
      (16%) 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 email is ok.

─ BiocCheck results ──
1 ERRORS | 6 WARNINGS | 16 NOTES

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