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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('chipenrich_2.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing chipenrich ───────────────────────────────────────────────────────
✔ Package installed successfully
── chipenrich session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpyJDudI/file658c6b891326/chipenrich
→ BiocVersion: 3.24
→ Package: chipenrich
→ PackageVersion: 2.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/chipenrich.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpyJDudI/file658c6b891326/chipenrich
→ installDir: /tmp/RtmpyJDudI/file658c63acba358
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on chipenrich ─────────────────────────────────────────────
* 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 3.4.0 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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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 (27%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • chipenrich-vignette.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/chipenrich-vignette.Rmd (chunk no. 16, line 302, column 118)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/chipenrich-vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of chipenrich...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/proxReg.R (line 250, column 42)
    • ...
    • R/test_binomial.R (line 41, column 45)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • plot_chipenrich_spline.R (line 110, column 30)
    • ...
    • utils.R (line 121, column 26)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/broadenrich.R (line 312, column 33)
    • ...
    • print() in R/proxReg.R (line 356, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/assign_peaks.R (line 28, column 14)
    • ...
    • R/utils.R (line 154, column 25)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/read.R (line 203, column 22)
    • ...
    • R/utils.R (line 77, column 22)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • T in R/proxReg.R (line 272, column 138)
    • F in R/test_polyapprox.R (line 87, column 60)
    • F in R/test_polyenrich.R (line 61, column 80)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • broadenrich.R (line 241, column 26)
    • ...
    • setup.R (line 163, column 28)
* 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 21
functions greater than 50 lines.
  The longest 5 functions are:
    • proxReg() (R/proxReg.R): 229 lines
    • ...
    • broadenrich() (R/broadenrich.R): 137 lines
* Checking man page documentation...





ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • hybridenrich.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 735 lines (13%) are > 80 characters long.
  First few lines:
    • R/assign_peaks.R#L3 #' Determine the midpoints of a set of i ...
    • ...
    • vignettes/chipenrich-vignette.Rmd#L427 5. T. Qin, C.T. Lee, R.G.
    Cavalcante, P. ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2260 lines (39%) contain tabs.
  First few lines:
    • R/assign_peaks.R#L23 #' peaks = peaks, ...
    • ...
    • vignettes/chipenrich-vignette.Rmd#L409 locusdef = "nearest_tss", qc_plots
    = FA ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 7 lines (0%) are not.
  First few lines:
    • R/hybrid.R#L199 ...
    • ...
    • R/utils.R#L135 as.numeric(num_peaks >= threshold); ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the chipenrich.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.