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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('StructuralVariantAnnotation_1.29.0.tar.gz','quit-with-status'=TRUE)"
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── Installing StructuralVariantAnnotation ──────────────────────────────────────
✔ Package installed successfully
── StructuralVariantAnnotation session metadata ────────────────────────────────
→ sourceDir: /tmp/Rtmp06Z2i7/file1482f24e4db3ed/StructuralVariantAnnotation
→ BiocVersion: 3.24
→ Package: StructuralVariantAnnotation
→ PackageVersion: 1.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/StructuralVariantAnnotation.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp06Z2i7/file1482f24e4db3ed/StructuralVariantAnnotation
→ installDir: /tmp/Rtmp06Z2i7/file1482f26b1a5d9e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on StructuralVariantAnnotation ────────────────────────────
* 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 4.1.0 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,
Alignment
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...
* 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 (69%).
* 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:
    • vignettes.Rmd
* Checking package installation calls in R code...
* Checking for library/require of StructuralVariantAnnotation...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/eventDetection.R (line 137, column 16)
    • ...
    • R/util.R (line 19, column 19)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • eventDetection.R (line 32, column 19)
    • eventDetection.R (line 122, column 66)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/BreakpointGRanges.R (line 100, column 10)
    • ...
    • R/unittesthelper.R (line 68, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/BreakpointGRanges.R (line 250, column 10)
    • ...
    • R/extensions-VCF.R (line 435, column 49)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • eventDetection.R (line 22, column 38)
    • eventDetection.R (line 116, column 38)
    • eventDetection.R (line 118, column 41)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
  • .Deprecated() in R/eventDetection.R (line 21, column 5)
  • .Deprecated() in R/eventDetection.R (line 113, column 5)
* 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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • .breakpointRanges() (R/extensions-VCF.R): 411 lines
    • ...
    • calculateReferenceHomology() (R/BreakpointGRanges.R): 53 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • calculateReferenceHomology.Rd
    • ...
    • simpleEventType.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; 398 lines (16%) are > 80 characters long.
  First few lines:
    • R/BreakpointGRanges.R#L12 #' @param selfPartnerSingleBreakends tre ...
    • ...
    • vignettes/vignettes.Rmd#L339 gr.circos <- colo829_bpgr[seqnames(colo8 ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1039 lines (41%) contain tabs.
  First few lines:
    • R/BreakpointGRanges.R#L113 # as.data.frame(localhits, row.names=N ...
    • ...
    • vignettes/vignettes.Rmd#L349 circle(biovizBase::hg19sub, geom='text' ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 131 lines (5%) are
not.
  First few lines:
    • R/BreakpointGRanges.R#L25 .assertValidBreakpointGRanges(gr, allo ...
    • ...
    • vignettes/vignettes.Rmd#L268 labs(title="NA12878 chr22 CREST and HY ...
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 14 NOTES
ℹ See the StructuralVariantAnnotation.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.