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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('phyloseq_1.57.0.tar.gz','quit-with-status'=TRUE)"
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── Installing phyloseq ─────────────────────────────────────────────────────────
✔ Package installed successfully
── phyloseq session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2s6xis/file2d28107a9304b6/phyloseq
→ BiocVersion: 3.24
→ Package: phyloseq
→ PackageVersion: 1.57.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/phyloseq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp2s6xis/file2d28107a9304b6/phyloseq
→ installDir: /tmp/Rtmp2s6xis/file2d2810520940d0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on phyloseq ───────────────────────────────────────────────
* 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 3.3.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: DataImport
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* 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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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:
    • phyloseq-analysis.Rmd
    • phyloseq-basics.Rmd
    • phyloseq-FAQ.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/phyloseq-analysis.Rmd
    • ...
    • vignettes/phyloseq-mixture-models.Rmd
* Checking package installation calls in R code...
* Checking for library/require of phyloseq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/distance-methods.R (line 357, column 11)
    • ...
    • R/plot-methods.R (line 714, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • distance-methods.R (line 357, column 18)
    • ...
    • transform_filter-methods.R (line 819, column 35)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/IO-methods.R (line 250, column 25)
    • ...
    • cat() in R/IO-methods.R (line 2307, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/distance-methods.R (line 104, column 7)
    • ...
    • R/validity-methods.R (line 73, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/transform_filter-methods.R (line 164, column 15)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/extend_vegan.R (line 252, column 17)
    • R/transform_filter-methods.R (line 1030, column 22)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • IO-methods.R (line 640, column 25)
    • ...
    • plot-methods.R (line 1171, column 34)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/transform_filter-methods.R (line 129, column 17)
! WARNING: .Deprecated / .Defunct usage (found 41 times)
  • .Deprecated() in R/deprecated_functions.R (line 65, column 32)
  • ...
  • .Deprecated() in R/ordination-methods.R (line 157, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/distance-methods.R (line 355, column 41)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressMessages() in R/extend_metagenomeSeq.R (line 60, column 13)
  • ...
  • suppressWarnings() in R/transform_filter-methods.R (line 234, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 19
functions greater than 50 lines.
  The longest 5 functions are:
    • plot_ordination() (R/plot-methods.R): 269 lines
    • ...
    • fastUniFrac() (R/distance-methods.R): 123 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/assign-otu_table.Rd
    • ...
    • man/show-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • access.Rd
    • ...
    • taxa_are_rows-methods.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; 1118 lines (8%) are > 80 characters long.
  First few lines:
    • R/allClasses.R#L8 #' Various standard subset and assignmen ...
    • ...
    • vignettes/phyloseq-mixture-models.Rmd#L172 Here is a bar plot showing the
    log2-fold ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2461 lines (17%) contain tabs.
  First few lines:
    • R/allClasses.R#L13 #' A single logical specifying the orie ...
    • ...
    • vignettes/phyloseq-mixture-models.Rmd#L51 Project Name:
    `Kostic_colorectal_cancer_ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1110 lines (8%) are
not.
  First few lines:
    • R/allPackage.R#L29 # data.table NSE operators and helpers ...
    • ...
    • vignettes/phyloseq-mixture-models.Rmd#L189 theme(axis.text.x =
    element_text(angle ...
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 19 NOTES
ℹ See the phyloseq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.