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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CNVPanelizer_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CNVPanelizer ─────────────────────────────────────────────────────
✔ Package installed successfully
── CNVPanelizer session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpEdm7ky/file776ab1a3a851d/CNVPanelizer
→ BiocVersion: 3.24
→ Package: CNVPanelizer
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CNVPanelizer.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpEdm7ky/file776ab1a3a851d/CNVPanelizer
→ installDir: /tmp/RtmpEdm7ky/file776ab705ce113
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CNVPanelizer ───────────────────────────────────────────
* 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 3.2.0 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', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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:
    • CNVPanelizer.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/CNVPanelizer.Rnw
* Checking package installation calls in R code...
* Checking for library/require of CNVPanelizer...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/FolderAnalysis_functions.R (line 197, column 28)
    • ...
    • R/server.R (line 45, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • FolderAnalysis_functions.R (line 267, column 28)
    • ...
    • SyntheticData.R (line 45, column 52)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/FolderAnalysis_functions.R (line 849, column 13)
    • ...
    • print() in R/server.R (line 244, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/FolderAnalysis_functions.R (line 31, column 15)
    • ...
    • R/SyntheticData.R (line 56, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/FolderAnalysis_functions.R (line 84, column 15)
    • ...
    • R/FolderAnalysis_functions.R (line 1182, column 15)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/FolderAnalysis_functions.R (line 491, column 3)
  • set.seed() in R/SyntheticData.R (line 26, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressMessages() in R/FolderAnalysis_functions.R (line 1137, column 13)
* 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:
    • CNVPanelizerServer() (R/server.R): 230 lines
    • ...
    • GetGeneRegionsBand() (R/FolderAnalysis_functions.R): 96 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • CNVPanelizer-package.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 61% of man
pages use at least one of these tags.
  Found in files:
    • BedToGenomicRanges.Rd
    • ...
    • WriteListToXLSX.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; 303 lines (7%) are > 80 characters long.
  First few lines:
    • R/FolderAnalysis_functions.R#L84 message(paste("Bai file not found. ...
    • ...
    • vignettes/CNVPanelizer.Rnw#L486 below the noise level for the number ...
ℹ NOTE: Consider 4 spaces instead of tabs; 8 lines (0%) contain tabs.
  First few lines:
    • R/FolderAnalysis_functions.R#L686 # print(paste("Robust is ", robust))
    ...
    • ...
    • man/SelectReferenceSetFromReadCounts.Rd#L33 Lower bound percentage (only
    to be ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1406 lines (31%) are
not.
  First few lines:
    • R/FolderAnalysis_functions.R#L6 ampliconC ...
    • ...
    • vignettes/CNVPanelizer.Rnw#L491 \caption{Description of the CNV detect
    ...
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 Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 18 NOTES
ℹ See the CNVPanelizer.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.