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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Clomial_1.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Clomial ──────────────────────────────────────────────────────────
✔ Package installed successfully
── Clomial session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpq6PF5z/file73d7b64d157b3/Clomial
→ BiocVersion: 3.24
→ Package: Clomial
→ PackageVersion: 1.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Clomial.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpq6PF5z/file73d7b64d157b3/Clomial
→ installDir: /tmp/Rtmpq6PF5z/file73d7b4a4423eb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Clomial ────────────────────────────────────────────────
* 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 2.10 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...
✖ 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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • Clonal_decomposition_by_Clomial.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • Clonal_decomposition_by_Clomial.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Clonal_decomposition_by_Clomial.Rnw
* Checking package installation calls in R code...
* Checking for library/require of Clomial...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • best.match.R (line 12, column 12)
    • ...
    • row.z.likelihood.R (line 7, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/choose.best.R (line 31, column 5)
    • ...
    • print() in R/rsub.R (line 37, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/Clomial.R (line 22, column 12)
    • R/Clomial.R (line 44, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/Clomial.generate.data.R (line 8, column 10)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • choose.best.R (line 40, column 21)
    • ...
    • compute.P.reparam.R (line 58, column 30)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/Clomial.R (line 90, column 27)
    • ...
    • system() in R/rsub.R (line 45, column 5)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Remove browser() statements (found 5 times)
  • browser() in R/compute.P.reparam.R (line 32, column 9)
  • ...
  • browser() in R/Phi.R (line 18, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • Clomial.iterate() (R/Clomial.iterate.R): 153 lines
    • ...
    • Clomial.generate.data() (R/Clomial.generate.data.R): 77 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/breastCancer.Rd
* Checking package NEWS...
* 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; 10 lines (0%) are > 80 characters long.
  First few lines:
    • R/Clomial.generate.data.R#L2 function(N, C, S, averageCoverage, mutFr ...
    • ...
    • vignettes/Clonal_decomposition_by_Clomial.Rnw#L7 %\VignetteIndexEntry{A
    likelihood maximi ...
ℹ NOTE: Consider 4 spaces instead of tabs; 190 lines (8%) contain tabs.
  First few lines:
    • R/choose.best.R#L11 ## or it can be a vector of characters ...
    • ...
    • man/compute.errors.Rd#L4 Computes the error of a Clomial model. ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 769 lines (34%) are
not.
  First few lines:
    • R/best.match.R#L3 ## Matches the columns of row m2 to th ...
    • ...
    • vignettes/Clonal_decomposition_by_Clomial.Rnw#L103 local optima. ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the Clomial.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.