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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('leapR_1.1.0.tar.gz','quit-with-status'=TRUE)"
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── Installing leapR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── leapR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvvFjpv/filec814732854a7e/leapR
→ BiocVersion: 3.24
→ Package: leapR
→ PackageVersion: 1.1.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/leapR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvvFjpv/filec814732854a7e/leapR
→ installDir: /tmp/RtmpvvFjpv/filec81474546c31d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on leapR ──────────────────────────────────────────────────
* 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 4.5.0 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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (17%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/examples.Rmd
    • vignettes/order-enrichment.Rmd
* Checking package installation calls in R code...
* Checking for library/require of leapR...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/enrichment_in_groups.R (line 118, column 21)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • T in R/enrichment_in_groups.R (line 108, column 51)
    • T in R/enrichment_in_groups.R (line 108, column 73)
    • T in R/enrichment_in_groups.R (line 118, column 58)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/drug_barplots.R (line 113, column 11)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • enrichment_in_groups() (R/enrichment_in_groups.R): 179 lines
    • ...
    • _anonymous_.45() (R/enrichment_in_abundance.R): 82 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • plot_leapr_bar.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; 17 lines (1%) are > 80 characters long.
  First few lines:
    • R/drug_barplots.R#L7 #' @param res_df A leapR df containing B ...
    • ...
    • vignettes/order-enrichment.Rmd#L92 colnames(protdata.enrichment.zt) <- pa
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 877 lines (30%) are
not.
  First few lines:
    • R/calcTTest.R#L36 stopifnot(is(eset,'SummarizedExperimen ...
    • ...
    • vignettes/order-enrichment.Rmd#L123 ggplot(aes(x=test_comparison, y= `p
    co ...
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 10 NOTES
ℹ See the leapR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.