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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('quantsmooth_1.79.0.tar.gz','quit-with-status'=TRUE)"
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── Installing quantsmooth ──────────────────────────────────────────────────────
✔ Package installed successfully
── quantsmooth session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpXzHhWM/file105fb0225f76ce/quantsmooth
→ BiocVersion: 3.24
→ Package: quantsmooth
→ PackageVersion: 1.79.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/quantsmooth.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpXzHhWM/file105fb0225f76ce/quantsmooth
→ installDir: /tmp/RtmpXzHhWM/file105fb0240f6fbf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on quantsmooth ────────────────────────────────────────────
* 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 2.10.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpXzHhWM/file105fb0225f76ce/quantsmooth/man/grid.chromosome.Rd'
* 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:
    • quantsmooth.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • quantsmooth.Rnw
* Checking package installation calls in R code...
* Checking for library/require of quantsmooth...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/quantsmoothplot.R (line 91, column 15)
    • R/quantsmoothplot.R (line 133, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • quantsmooth.R (line 40, column 38)
    • ...
    • quantsmoothplot.R (line 518, column 44)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/quantsmooth.R (line 14, column 11)
    • ...
    • R/quantsmoothplot.R (line 525, column 20)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/quantsmoothplot.R (line 293, column 13)
    • R/quantsmoothplot.R (line 401, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/quantsmooth.R (line 149, column 15)
    • R/quantsmooth.R (line 155, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • quantsmooth.R (line 20, column 20)
    • ...
    • quantsmoothplot.R (line 427, column 19)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • grid.chromosome() (R/quantsmoothplot.R): 108 lines
    • ...
    • quantsmooth.seg() (R/quantsmooth.R): 55 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • getChangedIdx.Rd
    • ...
    • scaleto.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; 210 lines (14%) are > 80 characters long.
  First few lines:
    • R/quantsmooth.R#L4 .quantsmooth<-function(intensities, smoo ...
    • ...
    • vignettes/quantsmooth.Rnw#L114 plotSmoothed(ill.cn[,1],ill.pos,ylim=c(1
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 68 lines (4%) contain tabs.
  First few lines:
    • R/quantsmooth.R#L188 if(missing(cols)) cols<-1:ncol(intensit ...
    • ...
    • man/quantsmooth.seg.rd#L30 plot(quantsmooth.seg(bac.cn[,1],lambda= ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 627 lines (41%) are
not.
  First few lines:
    • R/quantsmooth.R#L5 m<-length(intensities) ...
    • ...
    • vignettes/quantsmooth.Rnw#L60 ...
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 | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the quantsmooth.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.