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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CNVrd2_1.51.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CNVrd2 ───────────────────────────────────────────────────────────
✔ Package installed successfully
── CNVrd2 session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpskM5c6/file777405132e3a/CNVrd2
→ BiocVersion: 3.24
→ Package: CNVrd2
→ PackageVersion: 1.51.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CNVrd2.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpskM5c6/file777405132e3a/CNVrd2
→ installDir: /tmp/RtmpskM5c6/file777407e4c9ec1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CNVrd2 ─────────────────────────────────────────────────
* 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 3.0.0 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...
! WARNING: Invalid BiocViews term(s):
  • 'Clustering.': Did you mean 'Clustering'?
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: Clustering,
VariantAnnotation, 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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (44%).
* 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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • CNVrd2.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • CNVrd2.Rnw
* Checking package installation calls in R code...
* Checking for library/require of CNVrd2...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/countReadInWindow.R (line 9, column 19)
    • library() in R/plotPolymorphicRegion.R (line 260, column 7)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/emnormalCNV.R (line 131, column 28)
    • ...
    • R/identifyPolymorphicRegion.R (line 158, column 31)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • countReadInWindow.R (line 48, column 53)
    • ...
    • segmentSamplesUsingPopInformation.R (line 114, column 45)
✖ ERROR: Use double colon for qualified imports: 'pkg::foo()'
  Found in files:
    • countReadInWindow.R (line 102, column 72)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/countReadInWindow.R (line 13, column 37)
    • ...
    • R/segmentSamplesUsingPopInformation.R (line 88, column 36)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/calculateLDSNPandCNV.R (line 78, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/countReadInWindow.R (line 10, column 73)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • calculateLDSNPandCNV.R (line 121, column 30)
* 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 12
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.5() (R/plotPolymorphicRegion.R): 292 lines
    • ...
    • _anonymous_.2() (R/emnormalCNV.R): 199 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/groupBayesianCNVs.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/countReadInWindow-methods.Rd
    • ...
    • man/segmentSamplesUsingPopInformation-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • countReadInWindow.Rd
    • ...
    • segmentSamplesUsingPopInformation.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 19% of man
pages use at least one of these tags.
  Found in files:
    • countReadInWindow.Rd
    • ...
    • segmentSamples.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • countReadInWindow.Rd
    • ...
    • segmentSamples.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; 318 lines (9%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L22 setClass("clusteringCNVs", representatio ...
    • ...
    • vignettes/CNVrd2.Rnw#L452 If we use the option \emph{entireGene = ...
ℹ NOTE: Consider 4 spaces instead of tabs; 45 lines (1%) contain tabs.
  First few lines:
    • R/AllClasses.R#L12 validity=function(object){ ...
    • ...
    • man/groupBayesianCNVs.Rd#L16 heidel.diag = FALSE, leftLimit = NULL, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1099 lines (31%) are
not.
  First few lines:
    • R/AllClasses.R#L2 representation(windows = "numer ...
    • ...
    • vignettes/CNVrd2.Rnw#L440 typePlot = "SD") ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 6 WARNINGS | ℹ 19 NOTES
ℹ See the CNVrd2.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.