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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('VERSO_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing VERSO ────────────────────────────────────────────────────────────
✔ Package installed successfully
── VERSO session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRzypTY/file1529ad3badcadd/VERSO
→ BiocVersion: 3.24
→ Package: VERSO
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/VERSO.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpRzypTY/file1529ad3badcadd/VERSO
→ installDir: /tmp/RtmpRzypTY/file1529ad2b29d3d9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on VERSO ──────────────────────────────────────────────────
* 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...
* 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...
ℹ NOTE: License 'file LICENSE' unknown; refer to
$R_HOME/share/licenses/license.db
ℹ and https://choosealicense.com/appendix/ for more info.
* Checking for recommended DESCRIPTION fields...
* 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: Vignette(s) found with missing chunk labels
  Found in files:
    • v2_running_VERSO.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/v1_introduction.Rmd
    • vignettes/v2_running_VERSO.Rmd
* Checking package installation calls in R code...
* Checking for library/require of VERSO...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • frontend.R (line 247, column 22)
    • ...
    • utils.R (line 159, column 49)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/frontend.R (line 109, column 13)
    • cat() in R/inference.R (line 147, column 13)
    • cat() in R/inference.R (line 191, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/frontend.R (line 83, column 15)
    • ...
    • R/inference.R (line 343, column 16)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/frontend.R (line 109, column 103)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • VERSO() (R/frontend.R): 206 lines
    • ...
    • get.phylo() (R/utils.R): 56 lines
* Checking man page documentation...
* 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; 93 lines (9%) are > 80 characters long.
  First few lines:
    • R/frontend.R#L17 #' @param D Input data for the inference ...
    • ...
    • vignettes/v2_running_VERSO.Rmd#L67 We can plot the inferred phylogetic
    tree ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 77 lines (8%) are not.
  First few lines:
    • R/frontend.R#L58 alpha = NULL, ...
    • ...
    • vignettes/v2_running_VERSO.Rmd#L55 verbose = FALSE) ...
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 13 NOTES
ℹ See the VERSO.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.