##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SpotClean_1.15.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing SpotClean ────────────────────────────────────────────────────────
✔ Package installed successfully
── SpotClean session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpqUna2T/file1462b817d14f95/SpotClean
→ BiocVersion: 3.24
→ Package: SpotClean
→ PackageVersion: 1.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SpotClean.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpqUna2T/file1462b817d14f95/SpotClean
→ installDir: /tmp/RtmpqUna2T/file1462b87dfef2c8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpotClean ──────────────────────────────────────────────
* 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 4.2.0 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...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 2024/06/08
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (21%).
* 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:
    • SpotClean.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SpotClean...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/create_slide.R (line 79, column 23)
    • ...
    • R/create_slide.R (line 87, column 26)
* 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 8
functions greater than 50 lines.
  The longest 5 functions are:
    • .SpotClean() (R/decontamination.R): 173 lines
    • ...
    • createSlide() (R/create_slide.R): 64 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; 37 lines (2%) are > 80 characters long.
  First few lines:
    • R/mbrain_raw.R#L5 #' https://support.10xgenomics.com/spati ...
    • ...
    • vignettes/SpotClean.Rmd#L255 Ni, Z., Prasad, A., Chen, S. et al. Spot ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 202 lines (8%) are
not.
  First few lines:
    • R/convert_to_seurat.R#L60 assay = ...
    • ...
    • vignettes/SpotClean.Rmd#L147 " ...
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 9 NOTES
ℹ See the SpotClean.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.