##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SimBu_1.15.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing SimBu ────────────────────────────────────────────────────────────
✔ Package installed successfully
── SimBu session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPCDcrW/file13221b4872563/SimBu
→ BiocVersion: 3.24
→ Package: SimBu
→ PackageVersion: 1.15.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SimBu.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpPCDcrW/file13221b4872563/SimBu
→ installDir: /tmp/RtmpPCDcrW/file13221b603b8d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SimBu ──────────────────────────────────────────────────
* 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...
* 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 (31%).
* 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:
    • sfaira_vignette.Rmd
    • ...
    • simulator_scaling_factors.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SimBu...
* Checking coding practice...
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/dataset.R (line 487, column 13)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/simulator.R (line 79, column 9)
* 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 13
functions greater than 50 lines.
  The longest 5 functions are:
    • simulate_bulk() (R/simulator.R): 239 lines
    • ...
    • calc_scaling_vector() (R/simulator.R): 102 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • dataset_h5ad.Rd
    • ...
    • sfaira_overview.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
  Found in files:
    • dataset_sfaira_multiple.Rd
    • dataset_sfaira.Rd
    • sfaira_overview.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; 460 lines (15%) are > 80 characters long.
  First few lines:
    • R/access_sfaira.R#L3 #' If you want to download datasets from ...
    • ...
    • vignettes/simulator_scaling_factors.Rmd#L264 In our analysis we found,
    that Census is ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 921 lines (30%) are
not.
  First few lines:
    • R/access_sfaira.R#L17 tryCatch( ...
    • ...
    • vignettes/simulator_scaling_factors.Rmd#L259 run_parallel = TRUE ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 9 NOTES
ℹ See the SimBu.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.