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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scMultiSim_1.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scMultiSim ───────────────────────────────────────────────────────
✔ Package installed successfully
── scMultiSim session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpplIEPa/file12c7ea508e2c1c/scMultiSim
→ BiocVersion: 3.24
→ Package: scMultiSim
→ PackageVersion: 1.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scMultiSim.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpplIEPa/file12c7ea508e2c1c/scMultiSim
→ installDir: /tmp/RtmpplIEPa/file12c7ea4c8d8404
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scMultiSim ─────────────────────────────────────────────
* 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 4.4.0 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...
ℹ Bioconductor dependencies found in Imports & Depends (9%).
* 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:
    • options.Rmd
    • spatialCCI.Rmd
    • workflow.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/spatialCCI.Rmd (chunk no. 14, line 286, column 14)
    • ...
    • vignettes/workflow.Rmd (chunk no. 3, line 69, column 18)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/options.Rmd
    • vignettes/workflow.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scMultiSim...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • 1_main.R (line 272, column 36)
    • ...
    • 9.1_shiny.R (line 102, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/0_opts.R (line 365, column 38)
    • ...
    • cat() in R/9_meta.R (line 38, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/8_utils.R (line 51, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/8_utils.R (line 32, column 49)
    • F in R/8_utils.R (line 34, column 49)
    • T in R/9.1_shiny.R (line 6, column 55)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • 0_opts.R (line 213, column 21)
    • 2_sim.R (line 228, column 19)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 29 times)
  • <<- in R/3.1_spatial.R (line 135, column 13)
  • ...
  • <<- in R/3.2_dyngrn.R (line 72, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 30
functions greater than 50 lines.
  The longest 5 functions are:
    • .rnaSeqSpatial() (R/2_sim.R): 305 lines
    • ...
    • gene_corr_cci() (R/7_benchmark.R): 157 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/run_shiny.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • add_outliers.Rd
  • ...
  • True2ObservedCounts.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:
    • Get_1region_ATAC_correlation.Rd
    • True2ObservedCounts.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; 391 lines (5%) are > 80 characters long.
  First few lines:
    • R/0_opts.R#L34 sprintf("The value should be one of ...
    • ...
    • vignettes/workflow.Rmd#L117 scMultiSim provides various visualizatio ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2675 lines (37%) are
not.
  First few lines:
    • R/0_opts.R#L6 is.logical, ...
    • ...
    • vignettes/workflow.Rmd#L71 # ... other options ...
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 | ⚠ 4 WARNINGS | ℹ 14 NOTES
ℹ See the scMultiSim.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.