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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MicrobiotaProcess_1.25.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MicrobiotaProcess ────────────────────────────────────────────────
✔ Package installed successfully
── MicrobiotaProcess session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmpN76zxE/filed86343522a596/MicrobiotaProcess
→ BiocVersion: 3.24
→ Package: MicrobiotaProcess
→ PackageVersion: 1.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MicrobiotaProcess.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpN76zxE/filed86343522a596/MicrobiotaProcess
→ installDir: /tmp/RtmpN76zxE/filed8634429e1ef5
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MicrobiotaProcess ──────────────────────────────────────
* 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 4.0.0 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 (15%).
* 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:
    • MicrobiotaProcess.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpN76zxE/filed86343522a596/MicrobiotaProcess/vignettes/MicrobiotaProcess.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MicrobiotaProcess...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/method-mp_diff_analysis.R (line 632, column 5)
    • require() in R/method-mp_diff_analysis.R (line 699, column 5)
    • require() in R/plot-methods.R (line 1227, column 5)
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • method-mp_cal_dist.R (line 369, column 16)
    • plot-methods.R (line 1502, column 11)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/method-mp_fortify.R (line 89, column 9)
    • ...
    • print() in R/method-mp_fortify.R (line 111, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/method-io-utilities.R (line 367, column 11)
    • ...
    • R/plot-methods.R (line 795, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/method-accessor.R (line 672, column 17)
    • ...
    • R/method-mp_mantel.R (line 106, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/diff-ml-utilities.R (line 107, column 61)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 61 times)
  • suppressWarnings() in R/diff-analysis-utilities.R (line 39, column 12)
  • ...
  • suppressWarnings() in R/taxa_utilities.R (line 42, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 57
functions greater than 50 lines.
  The longest 5 functions are:
    • .internal_plot_abundance() (R/plot-methods.R): 325 lines
    • ...
    • .internal_mp_diff_clade() (R/method-mp_diff_clade.R): 232 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/data-hmp_aerobiosis_small.Rd
    • ...
    • man/mouse.time.mpse.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/as.treedata.Rd
    • ...
    • man/set_scale_theme.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • as.MPSE.Rd
    • ...
    • theme_taxbar.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 51% of man
pages use at least one of these tags.
  Found in files:
    • as.treedata.Rd
    • ...
    • theme_taxbar.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • as.treedata.Rd
    • ...
    • theme_taxbar.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; 1586 lines (8%) are > 80 characters long.
  First few lines:
    • R/AllClass.R#L16 # phyloseq <- methods::getClassDef("phyl ...
    • ...
    • vignettes/MicrobiotaProcess.Rmd#L690 Here is the output of sessionInfo()
    on t ...
ℹ NOTE: Consider 4 spaces instead of tabs; 286 lines (1%) contain tabs.
  First few lines:
    • R/AllClass.R#L180 sampleda="dataframeOrNull"), ...
    • ...
    • R/utilities.R#L198 column_to_rownames(var="rowname") ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3341 lines (17%) are
not.
  First few lines:
    • R/AllClass.R#L76 colData = NULL, ...
    • ...
    • vignettes/MicrobiotaProcess.Rmd#L677 anno.taxa.class = Phylum ...
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 | ⚠ 4 WARNINGS | ℹ 15 NOTES
ℹ See the MicrobiotaProcess.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.