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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CRImage_1.61.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CRImage ──────────────────────────────────────────────────────────
✔ Package installed successfully
── CRImage session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmprOzTHT/file7aabd425838dc/CRImage
→ BiocVersion: 3.24
→ Package: CRImage
→ PackageVersion: 1.61.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CRImage.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmprOzTHT/file7aabd425838dc/CRImage
→ installDir: /tmp/RtmprOzTHT/file7aabd4539917f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CRImage ────────────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmprOzTHT/file7aabd425838dc/CRImage/man/calculateCellularity.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmprOzTHT/file7aabd425838dc/CRImage/man/CRImage-internal.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmprOzTHT/file7aabd425838dc/CRImage/vignettes/CRImage.Rnw'
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
CopyNumberVariation, 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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (43%).
* 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:
    • CRImage.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • CRImage.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/CRImage.Rnw
* Checking package installation calls in R code...
* Checking for library/require of CRImage...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/correctCopyNumber.R (line 3, column 9)
    • require() in R/correctCopyNumber.R (line 4, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/correctCopyNumber.R (line 214, column 52)
    • ...
    • R/segmentImage.R (line 143, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • calculateOtsu.R (line 15, column 27)
    • ...
    • writeDensityImage.R (line 76, column 72)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/correctCopyNumber.R (line 12, column 25)
    • ...
    • print() in R/labelCells.R (line 294, column 41)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/calculateCellularity.R (line 8, column 26)
    • ...
    • R/writeDensityImage.R (line 82, column 117)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/classificationAperio.R (line 8, column 17)
    • ...
    • R/processAperio.R (line 54, column 58)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/labelCells.R (line 353, column 103)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 37 times)
  • <<- in R/labelCells.R (line 103, column 30)
  • ...
  • <<- in R/segmentImage.R (line 151, column 59)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 19
functions greater than 50 lines.
  The longest 5 functions are:
    • correctCopyNumber() (R/correctCopyNumber.R): 427 lines
    • ...
    • determineCellularity() (R/determineCellularity.R): 186 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/labelCells.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/CRImage-internal.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • labelCells.Rd
  • segmentImage.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; 305 lines (7%) are > 80 characters long.
  First few lines:
    • R/calculateCellularity.R#L2 function(filename="",image=NA,classifier ...
    • ...
    • vignettes/CRImage.Rnw#L214 The results of \Rfunction{correctCopyNum ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2621 lines (64%) contain tabs.
  First few lines:
    • R/calculateCellularity.R#L4 if(is.null(classifier)){ ...
    • ...
    • vignettes/CRImage.Rnw#L216 plotCorrectedCN(res, chr=1) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 131 lines (3%) are
not.
  First few lines:
    • man/calculateCellularity.Rd#L12 \item{filename}{A path to an image fil
    ...
    • ...
    • vignettes/CRImage.Rnw#L205 rnorm(100,0.5, 0.1)) ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 20 NOTES
ℹ See the CRImage.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.