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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('annotatr_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing annotatr ─────────────────────────────────────────────────────────
✔ Package installed successfully
── annotatr session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYhMbcs/file5534825cd02e7/annotatr
→ BiocVersion: 3.24
→ Package: annotatr
→ PackageVersion: 1.39.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/annotatr.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpYhMbcs/file5534825cd02e7/annotatr
→ installDir: /tmp/RtmpYhMbcs/file553481d3a214c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on annotatr ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.5.0 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: Coverage
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...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (53%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • annotatr-vignette.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/annotatr-vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of annotatr...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/build_annotations.R (line 531, column 9)
    • library() in R/build_annotations.R (line 541, column 9)
    • library() in R/build_annotations.R (line 829, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/build_annotations.R (line 80, column 63)
    • ...
    • R/utils.R (line 274, column 26)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/build_annotations.R (line 24, column 9)
    • ...
    • R/visualize.R (line 734, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/intersect.R (line 31, column 14)
    • ...
    • R/visualize.R (line 657, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • intersect.R (line 30, column 26)
    • intersect.R (line 34, column 30)
    • randomize.R (line 26, column 26)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/build_annotations.R (line 84, column 82)
  • ...
  • suppressWarnings() in R/build_annotations.R (line 96, column 80)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • build_gene_annots() (R/build_annotations.R): 309 lines
    • ...
    • plot_numerical_coannotations() (R/visualize.R): 100 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • expand_annotations.Rd
  • subset_order_tbl.Rd
  • tidy_annotations.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; 484 lines (16%) are > 80 characters long.
  First few lines:
    • R/annotatr_data_doc.R#L3 #' A \code{GRanges} of precomputed annot ...
    • ...
    • vignettes/annotatr-vignette.Rmd#L447 ```{r, fig.align='center',
    fig.cap='Basi ...
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 is registered at support site.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the annotatr.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.