##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DuplexDiscovereR_1.7.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing DuplexDiscovereR ─────────────────────────────────────────────────
✔ Package installed successfully
── DuplexDiscovereR session metadata ───────────────────────────────────────────
→ sourceDir: /tmp/RtmpBxq6Kw/file85a6d3555a82f/DuplexDiscovereR
→ BiocVersion: 3.24
→ Package: DuplexDiscovereR
→ PackageVersion: 1.7.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DuplexDiscovereR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpBxq6Kw/file85a6d3555a82f/DuplexDiscovereR
→ installDir: /tmp/RtmpBxq6Kw/file85a6d69eaf0a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DuplexDiscovereR ───────────────────────────────────────
* 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 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Alignment,
Classification, HiC
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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:
    • DuplexDiscovereR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of DuplexDiscovereR...
* Checking coding practice...
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/utils_annotation.R (line 280, column 14)
* 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 19
functions greater than 50 lines.
  The longest 5 functions are:
    • runDuplexDiscoverer() (R/runDuplexDiscoverer.R): 321 lines
    • ...
    • clusterDuplexGroups() (R/clusterDuplexGroups.R): 119 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • getRNAHybrids.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getRNAHybrids.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; 358 lines (7%) are > 80 characters long.
  First few lines:
    • R/clusterDuplexGroups.R#L13 #' @param min_arm_ratio For graph creati ...
    • ...
    • vignettes/DuplexDiscovereR.Rmd#L656 gi_clust_adj <-
    clusterDuplexGroups(gi_u ...
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 DuplexDiscovereR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.