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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('dar_1.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing dar ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── dar session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpiaH6RP/file7e1e865e189b5/dar
→ BiocVersion: 3.24
→ Package: dar
→ PackageVersion: 1.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/dar.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpiaH6RP/file7e1e865e189b5/dar
→ installDir: /tmp/RtmpiaH6RP/file7e1e843661dc8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on dar ────────────────────────────────────────────────────
* 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...
* 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:
    • article.Rmd
    • ...
    • import_export_recipes.Rmd
* Checking package installation calls in R code...
* Checking for library/require of dar...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bake.R (line 180, column 36)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/misc.R (line 640, column 83)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Defunct() in R/metagenomeseq.R (line 13, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/add_step.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/aldex2.R (line 150, column 18)
  • suppressMessages() in R/deseq2.R (line 149, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 18
functions greater than 50 lines.
  The longest 5 functions are:
    • definition() (R/recipe-class.R): 130 lines
    • ...
    • prep() (R/recipe-utils.R): 84 lines
* Checking man page documentation...
Registered S3 methods overwritten by 'vegan':
  method         from      
  reorder.hclust seriation 
  rev.hclust     dendextend
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • export_steps.Rd
  • step_metagenomeseq.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; 114 lines (2%) are > 80 characters long.
  First few lines:
    • R/ancom.R#L201 phyloseq::taxa_names(s_phy)[!p ...
    • ...
    • vignettes/filtering_subsetting.Rmd#L122 step_subset_taxa(rec, tax_level =
    "Kin ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1660 lines (25%) are
not.
  First few lines:
    • R/aldex2.R#L100 max_significance ...
    • ...
    • vignettes/import_export_recipes.Rmd#L52 step_maaslin() ...
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 | ⚠ 2 WARNINGS | ℹ 11 NOTES
ℹ See the dar.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.