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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('biomvRCNS_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing biomvRCNS ────────────────────────────────────────────────────────
✔ Package installed successfully
── biomvRCNS session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpeNQVQq/file5dd4a92e4fb9/biomvRCNS
→ BiocVersion: 3.24
→ Package: biomvRCNS
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/biomvRCNS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpeNQVQq/file5dd4a92e4fb9/biomvRCNS
→ installDir: /tmp/RtmpeNQVQq/file5dd4ade8ebfc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on biomvRCNS ──────────────────────────────────────────────
* 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: Coverage,
HiddenMarkovModel
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 (60%).
* 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:
    • biomvRCNS.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/biomvRCNS.Rnw (chunk no. 4, line 31, column 18)
    • ...
    • vignettes/biomvRCNS.Rnw (chunk no. 26, line 233, column 77)
* Checking package installation calls in R code...
* Checking for library/require of biomvRCNS...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/biomvRhsmm.R (line 58, column 25)
    • ...
    • require() in R/misc.R (line 91, column 25)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/biomvRhsmm.R (line 17, column 17)
    • ...
    • R/misc.R (line 416, column 28)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • biomvRhsmm.R (line 342, column 19)
    • ...
    • misc.R (line 336, column 42)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/biomvRhsmm.R (line 346, column 20)
    • ...
    • R/misc.R (line 67, column 24)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 16 times:
    • T in R/biomvRhsmm.R (line 54, column 57)
    • ...
    • T in R/misc.R (line 430, column 87)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • biomvRseg.R (line 10, column 57)
    • ...
    • misc.R (line 316, column 73)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/misc.R (line 53, column 33)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/biomvRhsmm.Rd
ℹ Found @ in vignettes/biomvRCNS.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
  The longest 5 functions are:
    • biomvRhsmm() (R/biomvRhsmm.R): 316 lines
    • ...
    • biomvRmgmr() (R/misc.R): 113 lines
* Checking man page documentation...
* 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; 567 lines (17%) are > 80 characters long.
  First few lines:
    • R/biomvRhsmm.R#L4 biomvRhsmm<-function(x, maxk=NULL, maxbp ...
    • ...
    • vignettes/biomvRCNS.Rnw#L451 mcols(cDMRs)<-DataFrame(cbind(TYPE='cDMR ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2060 lines (60%) contain tabs.
  First few lines:
    • R/biomvRhsmm.R#L5 ## input checking ...
    • ...
    • vignettes/biomvRCNS.Rnw#L452 by=list(cDMRs=subjectHits(idx)), FUN=me ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 195 lines (6%) are
not.
  First few lines:
    • R/biomvRhsmm.R#L394 maxk=as.integer(maxk), DL=as.i ...
    • ...
    • vignettes/biomvRCNS.Rnw#L433 prior.m='cluster', maxgap=100, com.emis ...
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 | ⚠ 6 WARNINGS | ℹ 13 NOTES
ℹ See the biomvRCNS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.