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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('mina_1.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing mina ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── mina session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpkFzrEo/filed9664cb288ee/mina
→ BiocVersion: 3.24
→ Package: mina
→ PackageVersion: 1.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/mina.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpkFzrEo/filed9664cb288ee/mina
→ installDir: /tmp/RtmpkFzrEo/filed96641f59a729
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mina ───────────────────────────────────────────────────
* 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 4.0.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Microbiome, Network
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: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/mina.Rmd
* Checking package installation calls in R code...
* Checking for library/require of mina...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/net_cls.R (line 146, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • adj.R (line 161, column 14)
    • ...
    • norm_tab.R (line 183, column 36)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/net_cls.R (line 176, column 20)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • T in R/dmr.R (line 24, column 35)
    • T in R/net_dis_indi.R (line 261, column 28)
    • T in R/net_dis_pcoa.R (line 45, column 59)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • check.R (line 15, column 26)
    • ...
    • fit_tabs.R (line 44, column 37)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/norm_tab.R (line 180, column 9)
  • suppressWarnings() in R/norm_tab.R (line 188, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.52() (R/net_dis_indi.R): 228 lines
    • ...
    • _anonymous_.16() (R/net_node_cmp.R): 94 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/data-hmp.Rd
    • man/data-maize.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/hmp_des.Rd
    • ...
    • man/net_node_cmp.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • cp_cor.Rd
  • ...
  • tina.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
  Found in files:
    • net_dis_indi.Rd
    • ...
    • tina.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • net_dis_indi.Rd
    • ...
    • tina.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; 20 lines (0%) are > 80 characters long.
  First few lines:
    • R/adj.R#L123 #' \href{https://github.com/defleury/Sch ...
    • ...
    • vignettes/mina.Rmd#L302 the *F* (the real distance) and *Fp* (th ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 912 lines (21%) are
not.
  First few lines:
    • R/adj.R#L25 function(x, method, sig = FALS ...
    • ...
    • vignettes/mina.Rmd#L243 ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | ℹ 20 NOTES
ℹ See the mina.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.