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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RareVariantVis_2.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RareVariantVis ───────────────────────────────────────────────────
✔ Package installed successfully
── RareVariantVis session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/RtmpDEYSqp/file10770755c8fcee/RareVariantVis
→ BiocVersion: 3.24
→ Package: RareVariantVis
→ PackageVersion: 2.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RareVariantVis.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpDEYSqp/file10770755c8fcee/RareVariantVis
→ installDir: /tmp/RtmpDEYSqp/file1077072ae43d5e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RareVariantVis ─────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
VariantAnnotation, CRISPR, DataImport
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (67%).
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • RareVariantsVis.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 5 out of 5 code chunks = 100% unevaluated
ℹ 
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/RareVariantsVis.Rnw
* Checking package installation calls in R code...
* Checking for library/require of RareVariantVis...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/callHomozygous.R (line 54, column 24)
    • ...
    • R/getCrisprGuides.R (line 33, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • callHomozygous.R (line 79, column 23)
    • ...
    • rareVariantVis.R (line 21, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/rareVariantVis.R (line 8, column 5)
    • ...
    • cat() in R/rareVariantVis.R (line 74, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/callHomozygous.R (line 9, column 16)
    • ...
    • R/rareVariantVis.R (line 69, column 23)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • chromosomeVis() (R/chromosomeVis.R): 864 lines
    • ...
    • movingAverage() (R/movingAverage.R): 54 lines
* Checking man page documentation...
Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘phastCons100way.UCSC.hg19’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • callHomozygous.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ 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...
ℹ NOTE: Consider shorter lines; 164 lines (10%) are > 80 characters long.
  First few lines:
    • R/callHomozygous.R#L12 centromeres_file = system.file("e ...
    • ...
    • vignettes/RareVariantsVis.Rnw#L162 Another feature of RareVariantVis2
    packa ...
ℹ NOTE: Consider 4 spaces instead of tabs; 9 lines (1%) contain tabs.
  First few lines:
    • R/chromosomeVis.R#L196 lo = lo[-overlapping] - 0.1 ...
    • ...
    • vignettes/RareVariantsVis.Rnw#L158 \label{Figure:interactive-vis} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 83 lines (5%) are not.
  First few lines:
    • R/callHomozygous.R#L13 ...
    • ...
    • vignettes/RareVariantsVis.Rnw#L165 "RareVariants_Coriell_S2. ...
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.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the RareVariantVis.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.