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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('OCplus_1.87.0.tar.gz','quit-with-status'=TRUE)"
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── Installing OCplus ───────────────────────────────────────────────────────────
✔ Package installed successfully
── OCplus session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpyfhqfB/filef8dc268e82f1e/OCplus
→ BiocVersion: 3.24
→ Package: OCplus
→ PackageVersion: 1.87.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/OCplus.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpyfhqfB/filef8dc268e82f1e/OCplus
→ installDir: /tmp/RtmpyfhqfB/filef8dc267cc312e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on OCplus ─────────────────────────────────────────────────
* 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 2.1.0 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...
* 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 (20%).
* 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:
    • OCplus.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • OCplus.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/OCplus.Rnw
* Checking package installation calls in R code...
* Checking for library/require of OCplus...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/OCshow.R (line 16, column 10)
    • R/OCshow.R (line 50, column 23)
    • R/OCshow.R (line 51, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • FDR.R (line 45, column 15)
    • ...
    • TOC.R (line 157, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/localfdr.R (line 91, column 9)
    • ...
    • cat() in R/localfdr2d.R (line 47, column 36)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/CDF.R (line 1, column 7)
    • ...
    • R/TOC.R (line 191, column 23)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/FDR.R (line 25, column 5)
    • F in R/FDR.R (line 78, column 11)
    • F in R/FDR.R (line 87, column 19)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • OCshow.R (line 34, column 29)
! WARNING: Remove set.seed usage (found 4 times)
  • set.seed() in R/FDR.R (line 43, column 25)
  • ...
  • set.seed() in R/localfdr2d.R (line 90, column 29)
* 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 15
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.1() (R/samplesize.R): 233 lines
    • ...
    • fdr1d() (R/localfdr1d.R): 101 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/DrawContourlines.Rd
    • ...
    • man/plot.fdr1d.result.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • DrawContourlines.Rd
  • tstatistics.Rd
  • Undocumented.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; 280 lines (7%) are > 80 characters long.
  First few lines:
    • R/CDF.R#L17 ret = p[1] * pt(x, df = n1+n2 - 2, n ...
    • ...
    • vignettes/OCplus.Rnw#L258 The estimated proportion \Robject{p0.est ...
ℹ NOTE: Consider 4 spaces instead of tabs; 33 lines (1%) contain tabs.
  First few lines:
    • R/localfdr.R#L137 if (inherits(x, "FDR.result")){ ...
    • ...
    • man/TOC.Rd#L12 nplot = 100, xlim, ylim = c(0, 1), main ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 264 lines (7%) are
not.
  First few lines:
    • R/CDF.R#L56 (CDFmix(x, n1, n2, pmix, D0, ...
    • ...
    • man/tstatistics.Rd#L20 \item{paired}{indicates whether to use ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 17 NOTES
ℹ See the OCplus.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.