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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('simona_1.11.0.tar.gz','quit-with-status'=TRUE)"
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── Installing simona ───────────────────────────────────────────────────────────
✔ Package installed successfully
── simona session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1eC6Rl/file1328131411c3c7/simona
→ BiocVersion: 3.24
→ Package: simona
→ PackageVersion: 1.11.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/simona.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp1eC6Rl/file1328131411c3c7/simona
→ installDir: /tmp/Rtmp1eC6Rl/file132813215d774d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on simona ─────────────────────────────────────────────────
* 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 4.1.0 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 (12%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of simona...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/anno_gene.R (line 35, column 51)
    • ...
    • R/reorder.R (line 222, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • 00_global.R (line 18, column 38)
    • ...
    • reorder.R (line 205, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/shiny.R (line 190, column 17)
    • print() in R/shiny.R (line 358, column 1)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/00_global.R (line 3, column 17)
    • ...
    • R/zzz.R (line 46, column 54)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 4 times)
  • <<- in R/00_global.R (line 13, column 35)
  • ...
  • <<- in R/tree.R (line 149, column 32)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressMessages() in R/go.R (line 66, column 17)
  • ...
  • suppressMessages() in R/utils.R (line 190, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 20
functions greater than 50 lines.
  The longest 5 functions are:
    • dag_circular_viz() (R/plot.R): 362 lines
    • ...
    • server() (R/shiny.R): 159 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/dag_shiny.Rd
    • man/ontology.Rd
    • man/print.print_source.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • add_annotation.Rd
  • ...
  • ontology.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
  Found in files:
    • dag_enrich_on_items.Rd
    • ...
    • partition_by_level.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • dag_enrich_on_items.Rd
    • ...
    • import_obo.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; 902 lines (9%) are > 80 characters long.
  First few lines:
    • R/00_global.R#L33 #' @param require_anno If it is set to ` ...
    • ...
    • R/utils.R#L186 exec_under_message_condition = function( ...
ℹ NOTE: Consider 4 spaces instead of tabs; 4690 lines (46%) contain tabs.
  First few lines:
    • R/00_global.R#L10 fun = get(method, envir = topenv(), inh ...
    • ...
    • R/zzz.R#L49 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 6 lines (0%) are not.
  First few lines:
    • R/transverse.R#L277 ...
    • ...
    • R/zzz.R#L38 reg.finalizer(parent, finalize, onexi ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 16 NOTES
ℹ See the simona.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.