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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ClustIRR_1.11.0.tar.gz','quit-with-status'=TRUE)"
###
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── Installing ClustIRR ─────────────────────────────────────────────────────────
✔ Package installed successfully
── ClustIRR session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpdN0w8m/file767e4695af544/ClustIRR
→ BiocVersion: 3.24
→ Package: ClustIRR
→ PackageVersion: 1.11.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ClustIRR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpdN0w8m/file767e4695af544/ClustIRR
→ installDir: /tmp/RtmpdN0w8m/file767e44a9a9c9f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ClustIRR ───────────────────────────────────────────────
* 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 4.3.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpdN0w8m/file767e4695af544/ClustIRR/man/get_beta_cprob_ag.Rd'
* 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 (13%).
* 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:
    • User_manual_groups.Rmd
    • User_manual_introduction.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/User_manual_groups.Rmd
    • vignettes/User_manual_introduction.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ClustIRR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/stanmodels.R (line 11, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dco.R (line 39, column 16)
    • ...
    • graph.R (line 385, column 14)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/input_check.R (line 103, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/community_motif.R (line 12, column 14)
    • ...
    • R/input_check.R (line 218, column 10)
* 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 26
functions greater than 50 lines.
  The longest 5 functions are:
    • get_posterior_summaries() (R/dco.R): 302 lines
    • ...
    • get_community_summary() (R/community.R): 102 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; 7 lines (0%) are > 80 characters long.
  First few lines:
    • R/community_honeycomb.R#L14 contrast = p ...
    • ...
    • vignettes/User_manual_introduction.Rmd#L426 ### **Quantitative**
    similarity between ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 740 lines (16%) are
not.
  First few lines:
    • R/annotation_utils.R#L14 "Antigen_speci ...
    • ...
    • vignettes/User_manual_introduction.Rmd#L685 stroke = 0.4, col = "whit ...
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 | ⚠ 0 WARNINGS | ℹ 12 NOTES
ℹ See the ClustIRR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.