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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scDesign3_1.11.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scDesign3 ────────────────────────────────────────────────────────
✔ Package installed successfully
── scDesign3 session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplINQM7/file12a87d7eb07a9b/scDesign3
→ BiocVersion: 3.24
→ Package: scDesign3
→ PackageVersion: 1.11.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scDesign3.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmplINQM7/file12a87d7eb07a9b/scDesign3
→ installDir: /tmp/RtmplINQM7/file12a87d4baf6b84
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scDesign3 ──────────────────────────────────────────────
* 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...
ℹ Bioconductor dependencies found in Imports & Depends (14%).
* 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:
    • scDesign3.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scDesign3...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/construct_data.R (line 195, column 26)
    • ...
    • R/plot_reduceddim.R (line 55, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • fit_copula.R (line 643, column 13)
    • ...
    • sparse_cov.R (line 208, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/fit_copula.R (line 294, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/extract_para.R (line 152, column 19)
    • ...
    • R/sparse_cov.R (line 144, column 12)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/fit_copula.R (line 161, column 15)
    • ...
    • R/simu_new.R (line 156, column 19)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/fit_marginal.R (line 525, column 30)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • extract_para.R (line 275, column 26)
    • ...
    • simu_new.R (line 324, column 26)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/fit_marginal.R (line 218, column 12)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressMessages() in R/extract_para.R (line 279, column 12)
  • ...
  • suppressMessages() in R/fit_marginal.R (line 694, column 34)
* 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:
    • fit_marginal() (R/fit_marginal.R): 675 lines
    • ...
    • predict.gamlss() (R/gamlss_fix.R): 258 lines
* Checking man page documentation...
Registered S3 method overwritten by 'gamlss':
  method   from
  print.ri bit 
Registered S3 method overwritten by 'scDesign3':
  method         from  
  predict.gamlss gamlss
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • plot_reduceddim.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; 429 lines (10%) are > 80 characters long.
  First few lines:
    • R/construct_data.R#L7 #' (explanatory variables) and the expre ...
    • ...
    • vignettes/scDesign3.Rmd#L117 simu_sce <- SingleCellExperiment(list(co ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2042 lines (46%) are
not.
  First few lines:
    • R/construct_data.R#L49 assay_use = " ...
    • ...
    • vignettes/scDesign3.Rmd#L130 n_pc = ...
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 16 NOTES
ℹ See the scDesign3.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.