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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('metapone_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing metapone ─────────────────────────────────────────────────────────
✔ Package installed successfully
── metapone session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpdi67iT/filed4b47234e32af/metapone
→ BiocVersion: 3.24
→ Package: metapone
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/metapone.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpdi67iT/filed4b47234e32af/metapone
→ installDir: /tmp/Rtmpdi67iT/filed4b475d3ea731
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on metapone ───────────────────────────────────────────────
* 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 4.1.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpdi67iT/filed4b47234e32af/metapone/man/metapone.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmpdi67iT/filed4b47234e32af/metapone/man/ptable.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Regression,
GeneExpression, DifferentialExpression, GeneSetEnrichment
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...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 2022-8-20
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (25%).
* 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:
    • metapone.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/metapone.Rmd
* Checking package installation calls in R code...
* Checking for library/require of metapone...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bbplot1d.R (line 5, column 47)
    • ...
    • metapone.R (line 314, column 35)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bbplot1d.R (line 6, column 11)
    • ...
    • R/metapone.R (line 322, column 21)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/bbplot1d.R (line 7, column 102)
    • T in R/bbplot2d.R (line 8, column 102)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/metapone.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • metapone() (R/metapone.R): 356 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/bbplot1d.Rd
    • man/bbplot2d.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 99 lines (9%) are > 80 characters long.
  First few lines:
    • R/bbplot1d.R#L1 globalVariables(c("p_value","logp", "lfd ...
    • ...
    • vignettes/metapone.Rmd#L92 We note that applying the multiple-match ...
ℹ NOTE: Consider 4 spaces instead of tabs; 45 lines (4%) contain tabs.
  First few lines:
    • R/AllGenerics.R#L8 ...
    • ...
    • man/ptable.Rd#L21 and pathway name.  ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 296 lines (27%) are
not.
  First few lines:
    • R/AllGenerics.R#L2 def=function(obje ...
    • ...
    • vignettes/metapone.Rmd#L13 comment = "#>" ...
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 18 NOTES
ℹ See the metapone.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.