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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('benchdamic_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing benchdamic ───────────────────────────────────────────────────────
✔ Package installed successfully
── benchdamic session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpo3L2eD/file5a6f860f925da/benchdamic
→ BiocVersion: 3.24
→ Package: benchdamic
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/benchdamic.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpo3L2eD/file5a6f860f925da/benchdamic
→ installDir: /tmp/Rtmpo3L2eD/file5a6f861be6a69
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on benchdamic ─────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (47%).
* 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:
    • intro.Rmd
* Checking package installation calls in R code...
* Checking for library/require of benchdamic...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • concordance.R (line 511, column 33)
    • ...
    • concordance.R (line 514, column 39)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/DA_ANCOM.R (line 159, column 15)
    • ...
    • R/DA_mixMC.R (line 137, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 24 times)
  • suppressMessages() in R/DA_ALDEx2.R (line 218, column 21)
  • ...
  • suppressWarnings() in R/plotTIEC.R (line 399, column 27)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 36
functions greater than 50 lines.
  The longest 5 functions are:
    • DA_maaslin3() (R/DA_Maaslin3.R): 224 lines
    • ...
    • DA_metagenomeSeq() (R/DA_metagenomeSeq.R): 140 lines
* Checking man page documentation...
Registered S3 method overwritten by 'rmutil':
  method         from
  print.response httr
Registered S3 method overwritten by 'gplots':
  method         from     
  reorder.factor DescTools
Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
Also defined by ‘spam’
* 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; 241 lines (2%) are > 80 characters long.
  First few lines:
    • R/DA_linda.R#L130 #' base_linda <- set_linda(formula = "~ ...
    • ...
    • vignettes/intro.Rmd#L1877 Secondly, thanks to methods like `plotMu ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 290 lines (3%) are
not.
  First few lines:
    • R/concordance.R#L92 " balanced subsets. Ple ...
    • ...
    • vignettes/intro.Rmd#L927 N = 2 ...
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 | ⚠ 0 WARNINGS | ℹ 12 NOTES
ℹ See the benchdamic.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.