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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scFeatures_1.13.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scFeatures ───────────────────────────────────────────────────────
✔ Package installed successfully
── scFeatures session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPfSm21/file12accd7daee26a/scFeatures
→ BiocVersion: 3.24
→ Package: scFeatures
→ PackageVersion: 1.13.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scFeatures.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpPfSm21/file12accd7daee26a/scFeatures
→ installDir: /tmp/RtmpPfSm21/file12accddbe21ba
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scFeatures ─────────────────────────────────────────────
* 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...
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (28%).
* 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:
    • scFeatures_overview.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scFeatures...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • helper_celltype_expression.R (line 26, column 35)
    • ...
    • helper_celltype_expression.R (line 460, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/run_scfeatures.R (line 319, column 9)
    • ...
    • print() in R/wrapper_run_scfeatures.R (line 214, column 5)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/helper_pathway.R (line 179, column 73)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/get_num_cell_per_spot.Rd
ℹ Found @ in man/remove_mito_ribo.Rd
ℹ Found @ in man/run_CCI.Rd
ℹ Found @ in man/run_celltype_interaction.Rd
ℹ Found @ in man/run_gene_cor_celltype.Rd
ℹ Found @ in man/run_gene_cor.Rd
ℹ Found @ in man/run_gene_mean_celltype.Rd
ℹ Found @ in man/run_gene_mean.Rd
ℹ Found @ in man/run_gene_prop_celltype.Rd
ℹ Found @ in man/run_gene_prop.Rd
ℹ Found @ in man/run_L_function.Rd
ℹ Found @ in man/run_Morans_I.Rd
ℹ Found @ in man/run_nn_correlation.Rd
ℹ Found @ in man/run_pathway_gsva.Rd
ℹ Found @ in man/run_pathway_mean.Rd
ℹ Found @ in man/run_pathway_prop.Rd
ℹ Found @ in man/run_proportion_logit.Rd
ℹ Found @ in man/run_proportion_ratio.Rd
ℹ Found @ in man/run_proportion_raw.Rd
ℹ Found @ in man/scFeatures.Rd
ℹ Found @ in vignettes/scFeatures_overview.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 13 times)
  • suppressMessages() in R/helper_CCI.R (line 52, column 5)
  • ...
  • suppressMessages() in R/run_scfeatures.R (line 486, column 25)
* 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:
    • scFeatures() (R/wrapper_run_scfeatures.R): 150 lines
    • ...
    • helper_nncorr_protein() (R/helper_spatial_metrics.R): 79 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • run_association_study_report.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • run_association_study_report.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • run_association_study_report.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 222 lines (5%) are > 80 characters long.
  First few lines:
    • R/data.R#L27 #' A list with two dataframes. In each d ...
    • ...
    • vignettes/scFeatures_overview.Rmd#L180 Inside the directory defined in
    the `out ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 394 lines (9%) are
not.
  First few lines:
    • R/helper_bulk_expression.R#L8 ...
    • ...
    • vignettes/scFeatures_overview.Rmd#L121 ...
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 | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the scFeatures.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.