##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('compSPOT_1.11.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing compSPOT ─────────────────────────────────────────────────────────
✔ Package installed successfully
── compSPOT session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpjcoUtc/file78b501681e534/compSPOT
→ BiocVersion: 3.24
→ Package: compSPOT
→ PackageVersion: 1.11.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/compSPOT.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpjcoUtc/file78b501681e534/compSPOT
→ installDir: /tmp/RtmpjcoUtc/file78b5044b75ec
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on compSPOT ───────────────────────────────────────────────
* 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 4.3.0 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...
! 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • compSPOT-vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of compSPOT...
* Checking coding practice...
* 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 6
functions greater than 50 lines.
  The longest 5 functions are:
    • find_hotspots() (R/find_hotspots.R): 127 lines
    • ...
    • plot_features() (R/compare_features.R): 70 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; 16 lines (1%) are > 80 characters long.
  First few lines:
    • R/compare_features.R#L16 #' @return ggplot objects of comparison ...
    • ...
    • vignettes/compSPOT-vignette.Rmd#L201 ## EDA of Mutation Hotspot Burden
    and Pe ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 363 lines (24%) are
not.
  First few lines:
    • R/compare_features.R#L29 df <- na.omit(df) ...
    • ...
    • vignettes/compSPOT-vignette.Rmd#L190 include_gen ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 7 NOTES
ℹ See the compSPOT.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.