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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GenVisR_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GenVisR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── GenVisR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpO87wyF/filea5335a7c1437/GenVisR
→ BiocVersion: 3.24
→ Package: GenVisR
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GenVisR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpO87wyF/filea5335a7c1437/GenVisR
→ installDir: /tmp/RtmpO87wyF/filea53357bf72a9e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GenVisR ────────────────────────────────────────────────
* 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 3.3.0 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...
* 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 (50%).
* 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:
    • Intro.Rmd
    • waterfall_introduction.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/waterfall_introduction.Rmd
* Checking package installation calls in R code...
* Checking for library/require of GenVisR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cnFreq_qual.R (line 46, column 24)
    • ...
    • R/VEP-class.R (line 319, column 48)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • compIdent_bamRcnt.R (line 98, column 28)
    • ...
    • VEP_Virtual-class.R (line 140, column 39)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/MutationAnnotationFormat_v2.1-class.R (line 18, column 14)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Clinical-class.R (line 159, column 30)
    • ...
    • R/multi_align.R (line 19, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/lohSpec_qual.R (line 28, column 16)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • F in R/cnFreq_qual.R (line 46, column 83)
    • ...
    • F in R/Waterfall-class.R (line 1331, column 105)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/cnFreq.R (line 99, column 22)
  • ...
  • suppressWarnings() in R/VEP-class.R (line 73, column 24)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 36
functions greater than 50 lines.
  The longest 5 functions are:
    • geneViz() (R/geneViz.R): 194 lines
    • ...
    • genCov() (R/genCov.R): 136 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/Clinical-class.Rd
    • ...
    • man/writeData-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • Clinical-class.Rd
    • ...
    • writeData-methods.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; 1314 lines (8%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L57 def=function(object, labelColumn, ve ...
    • ...
    • vignettes/waterfall_introduction.Rmd#L353 ```{r, fig.keep='last',
    fig.width=10, fi ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 5667 lines (36%) are
not.
  First few lines:
    • R/Clinical-class.R#L20 representation=representation(c ...
    • ...
    • vignettes/waterfall_introduction.Rmd#L208 '20-30', '31-50 ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the GenVisR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.