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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ctc_1.87.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ctc ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── ctc session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpIMGCsf/file7bb1c22f1b0c4/ctc
→ BiocVersion: 3.24
→ Package: ctc
→ PackageVersion: 1.87.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ctc.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpIMGCsf/file7bb1c22f1b0c4/ctc
→ installDir: /tmp/RtmpIMGCsf/file7bb1c737a5b4e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ctc ────────────────────────────────────────────────────
* 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...
* 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...
! 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:
    • ctc.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ctc.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ctc.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ctc...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/zzz.R (line 7, column 7)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • r2cluster.R (line 34, column 31)
    • ...
    • xcluster2r.R (line 158, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/hclust2treeview.R (line 14, column 14)
    • R/hclust2treeview.R (line 16, column 16)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/read.eisen.R (line 7, column 16)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/xcluster.R (line 58, column 5)
    • ...
    • system() in R/xcluster.R (line 82, column 1)
* 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 6
functions greater than 50 lines.
  The longest 5 functions are:
    • xcluster2r() (R/xcluster2r.R): 187 lines
    • ...
    • r2xcluster() (R/r2xcluster.R): 73 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/r2cluster.Rd
    • man/r2gtr.Rd
    • man/r2xcluster.Rd
Loading required package: amap
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • read.eisen.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • r2xcluster.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • r2xcluster.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; 48 lines (3%) are > 80 characters long.
  First few lines:
    • R/hc2Newick.R#L35 return(paste("(", left, ":", dist/ ...
    • ...
    • vignettes/ctc.Rnw#L133 made by Gavin Scherlock, http://genome- ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
  First few lines:
    • R/r2gtr.R#L6 # Created : 20/11/02 ...
    • ...
    • R/xcluster2r.R#L174 { ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 279 lines (19%) are
not.
  First few lines:
    • R/hc2Newick.R#L3 dist <- 0 ...
    • ...
    • vignettes/ctc.Rnw#L146 for Huge Clustering}, R News, 2006, vo ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the ctc.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.