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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scPipe_2.13.1.tar.gz','quit-with-status'=TRUE)"
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── Installing scPipe ───────────────────────────────────────────────────────────
✔ Package installed successfully
── scPipe session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpCpW1HE/file12cd5f74e81bd0/scPipe
→ BiocVersion: 3.24
→ Package: scPipe
→ PackageVersion: 2.13.1
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scPipe.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpCpW1HE/file12cd5f74e81bd0/scPipe
→ installDir: /tmp/RtmpCpW1HE/file12cd5f3f44f472
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scPipe ─────────────────────────────────────────────────
* 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 (36%).
* 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:
    • scPipe_atac_tutorial.Rmd
    • scPipe_tutorial.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scPipe...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/anno_import.R (line 171, column 9)
    • R/qc.R (line 389, column 76)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/sc_atac_create_fragments.R (line 76, column 12)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/biomart_methods.R (line 42, column 33)
* 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 23
functions greater than 50 lines.
  The longest 5 functions are:
    • sc_atac_feature_counting() (R/sc_atac_feature_counting.R): 663 lines
    • ...
    • sc_atac_pipeline() (R/sc_atac_pipeline.R): 130 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/sc_atac_cell_calling.Rd
    • man/sc_atac_emptydrops_cell_calling.Rd
    • man/sc_atac_filter_cell_calling.Rd


✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • anno_to_saf.Rd
    • ...
    • TF.IDF.custom.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 31% of man
pages use at least one of these tags.
  Found in files:
    • anno_to_saf.Rd
    • ...
    • sc_trim_barcode.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • anno_to_saf.Rd
    • ...
    • sc_trim_barcode.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; 710 lines (11%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L15 setGeneric("QC_metrics<-", function(obje ...
    • ...
    • vignettes/scPipe_tutorial.Rmd#L160 Since the **scater** and **scran**
    packa ...
ℹ NOTE: Consider 4 spaces instead of tabs; 124 lines (2%) contain tabs.
  First few lines:
    • R/sc_atac_trim_barcode.R#L122 write_gz <- TRUE ...
    • ...
    • R/sc_atac_trim_barcode.R#L257 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 94 lines (1%) are not.
  First few lines:
    • R/qc.R#L570 stop("No outlier information. Plea ...
    • ...
    • vignettes/scPipe_tutorial.Rmd#L70 output_file=file.path(data_dir, "out.a
    ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 14 NOTES
ℹ See the scPipe.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.