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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('cnvGSA_1.57.0.tar.gz','quit-with-status'=TRUE)"
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── Installing cnvGSA ───────────────────────────────────────────────────────────
✔ Package installed successfully
── cnvGSA session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpw5lAtf/file774502c5abca2/cnvGSA
→ BiocVersion: 3.24
→ Package: cnvGSA
→ PackageVersion: 1.57.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/cnvGSA.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpw5lAtf/file774502c5abca2/cnvGSA
→ installDir: /tmp/Rtmpw5lAtf/file77450325d68aa
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on cnvGSA ─────────────────────────────────────────────────
* 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:
CopyNumberVariation, Sequencing, GenotypingArray, Coverage, VariantAnnotation,
QualityControl, Regression
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 (17%).
* 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:
    • cnvGSA-vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/cnvGSA-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of cnvGSA...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/cnvGSA.R (line 2, column 1)
    • ...
    • library() in R/cnvGSA.R (line 5, column 1)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/cnvGSA.R (line 105, column 29)
    • ...
    • R/enrFiles.R (line 101, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cnvGSA.R (line 176, column 63)
    • ...
    • enrFiles.R (line 107, column 30)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/cnvGSA.R (line 82, column 9)
    • ...
    • cat() in R/enrFiles.R (line 134, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/cnvGSA.R (line 500, column 30)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 87 times:
    • T in R/cnvGSA.R (line 26, column 53)
    • ...
    • F in R/cnvGSAviz.R (line 91, column 82)
* 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 8
functions greater than 50 lines.
  The longest 5 functions are:
    • f.makeViz() (R/cnvGSAviz.R): 403 lines
    • ...
    • f.testGLM_unit() (R/cnvGSA.R): 84 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • CnvGSAInput-class.Rd
    • ...
    • f.makeViz.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; 283 lines (15%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L26 new( "CnvGSAInput", config.ls = conf ...
    • ...
    • vignettes/cnvGSA-vignette.Rnw#L37 In \texttt{cnvGSA}, subjects are
    treated ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1105 lines (60%) contain tabs.
  First few lines:
    • R/AllClasses.R#L6 representation( ...
    • ...
    • vignettes/cnvGSA-vignette.Rnw#L21 The Centre for Applied Genomics\\ \text
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 14 lines (1%) are not.
  First few lines:
    • R/enrFiles.R#L128 ...
    • ...
    • man/CnvGSAOutput-class.Rd#L38 } ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the cnvGSA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.