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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SeqSQC_1.35.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SeqSQC ───────────────────────────────────────────────────────────
✔ Package installed successfully
── SeqSQC session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmptpjAfM/file12fd2c12eeff64/SeqSQC
→ BiocVersion: 3.24
→ Package: SeqSQC
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SeqSQC.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmptpjAfM/file12fd2c12eeff64/SeqSQC
→ installDir: /tmp/RtmptpjAfM/file12fd2c6a94e7c9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SeqSQC ─────────────────────────────────────────────────
* 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 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ ExperimentData
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
! WARNING: Invalid BiocViews term(s):
  • 'Experiment Data': Did you mean 'ExperimentData'?
  • 'Sequencing Data': Did you mean 'SequencingData'?
* Checking for recommended biocViews...
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 (38%).
* 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...
! WARNING: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • vignette.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SeqSQC...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • IBDCheck.R (line 183, column 37)
    • ...
    • plotPop.R (line 11, column 31)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/sampleQC.R (line 99, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/IBDRemove.R (line 90, column 19)
    • R/problemList.R (line 58, column 23)
    • R/sampleQC.R (line 183, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/plotQCData.R (line 7, column 52)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • readgdsn.R (line 5, column 27)
* 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 11
functions greater than 50 lines.
  The longest 5 functions are:
    • LoadVfile() (R/LoadVfile.R): 169 lines
    • ...
    • PCACheck() (R/PCACheck.R): 126 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/CCDS.Hs37.3.reduced_chr1.bed.Rd
    • ...
    • man/sampleAnnotation.txt.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/SeqSQC-package.Rd
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘SeqSQC’
Warning: replacing previous import ‘S4Vectors::rename’ by ‘plotly::rename’ when loading ‘SeqSQC’
Warning: replacing previous import ‘IRanges::slice’ by ‘plotly::slice’ when loading ‘SeqSQC’
Warning: replacing previous import ‘ggplot2::last_plot’ by ‘plotly::last_plot’ when loading ‘SeqSQC’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • sampleQC.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • sampleQC.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • sampleQC.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; 136 lines (5%) are > 80 characters long.
  First few lines:
    • R/IBDCheck.R#L55 #' seqfile <- IBDCheck(seqfile, remove.s ...
    • ...
    • vignettes/vignette.Rmd#L243 Posting a question and tagging with “Seq ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 122 lines (5%) are
not.
  First few lines:
    • R/IBDCheck.R#L62 kin.filter = TRUE, ...
    • ...
    • R/zzz.R#L9 "sexinb ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 5 WARNINGS | ℹ 15 NOTES
ℹ See the SeqSQC.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.