##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('peakCombiner_1.3.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing peakCombiner ─────────────────────────────────────────────────────
✔ Package installed successfully
── peakCombiner session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpmLuhRf/filefdd166413d852/peakCombiner
→ BiocVersion: 3.24
→ Package: peakCombiner
→ PackageVersion: 1.3.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/peakCombiner.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpmLuhRf/filefdd166413d852/peakCombiner
→ installDir: /tmp/RtmpmLuhRf/filefdd16483cff31
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on peakCombiner ───────────────────────────────────────────
* 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 4.5.0 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (23%).
* 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:
    • peakCombiner.Rmd
* Checking package installation calls in R code...
* Checking for library/require of peakCombiner...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • centerExpandRegions.R (line 553, column 34)
    • prepareInputRegionsHelper.R (line 82, column 30)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/centerExpandRegions.R (line 560, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/centerExpandRegions.R (line 459, column 9)
  • ...
  • suppressWarnings() in R/filterRegionsHelper.R (line 404, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 16
functions greater than 50 lines.
  The longest 5 functions are:
    • centerExpandRegions() (R/centerExpandRegions.R): 511 lines
    • ...
    • combineRegions() (R/combineRegions.R): 262 lines
* Checking man page documentation...
* 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; 151 lines (3%) are > 80 characters long.
  First few lines:
    • R/centerExpandRegions.R#L85 #' @param genome Character value to ...
    • ...
    • vignettes/peakCombiner.Rmd#L952 We recommend to use the `nearest` option
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2096 lines (38%) are
not.
  First few lines:
    • R/centerExpandRegions.R#L152 center ...
    • ...
    • vignettes/peakCombiner.Rmd#L948 showMessages = FALSE ...
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 | ⚠ 0 WARNINGS | ℹ 10 NOTES
ℹ See the peakCombiner.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.