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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('AnnotationFilter_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing AnnotationFilter ─────────────────────────────────────────────────
✔ Package installed successfully
── AnnotationFilter session metadata ───────────────────────────────────────────
→ sourceDir: /tmp/RtmpmLGcAg/file1a76481d51e8d3/AnnotationFilter
→ BiocVersion: 3.24
→ Package: AnnotationFilter
→ PackageVersion: 1.37.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/AnnotationFilter.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpmLGcAg/file1a76481d51e8d3/AnnotationFilter
→ installDir: /tmp/RtmpmLGcAg/file1a764825f1489d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on AnnotationFilter ───────────────────────────────────────
* 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 3.4.0 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: GeneExpression
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (25%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of AnnotationFilter...
* Checking coding practice...
! WARNING: .Deprecated / .Defunct usage (found 2 times)
  • .Deprecated() in R/AnnotationFilter.R (line 574, column 5)
  • .Deprecated() in R/AnnotationFilterList.R (line 136, column 9)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • GenenameFilter.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; 3 lines (0%) are > 80 characters long.
  First few lines:
    • R/AnnotationFilterList.R#L65 txt <- c(txt, "length of 'lo ...
    • R/translate-utils.R#L52 stop('Arguments to "!" must ...
    • vignettes/AnnotationFilter.Rmd#L7 %\VignetteIndexEntry{Facilities for ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 30 lines (2%) are not.
  First few lines:
    • R/AnnotationFilter.R#L166 "<", ">=" ...
    • ...
    • vignettes/AnnotationFilter.Rmd#L351 x) ...
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...
ℹ Maintainer email is ok.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 7 NOTES
ℹ See the AnnotationFilter.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.