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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('bayNorm_1.31.0.tar.gz','quit-with-status'=TRUE)"
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── Installing bayNorm ──────────────────────────────────────────────────────────
✔ Package installed successfully
── bayNorm session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplGeBXX/file598444f6f75ce/bayNorm
→ BiocVersion: 3.24
→ Package: bayNorm
→ PackageVersion: 1.31.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/bayNorm.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmplGeBXX/file598444f6f75ce/bayNorm
→ installDir: /tmp/RtmplGeBXX/file598441ff7a83d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on bayNorm ────────────────────────────────────────────────
* 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 3.5 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...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (17%).
* 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:
    • bayNorm.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmplGeBXX/file598444f6f75ce/bayNorm/vignettes/bayNorm.Rmd
* Checking package installation calls in R code...
* Checking for library/require of bayNorm...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bayNorm.r (line 209, column 16)
    • ...
    • R/PRIOR_FUNCTIONS.R (line 499, column 28)
* 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 8
functions greater than 50 lines.
  The longest 5 functions are:
    • bayNorm() (R/bayNorm.r): 244 lines
    • ...
    • NOISY_FUN() (R/noisygene_detection.r): 76 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 22% of man
pages use at least one of these tags.
  Found in files:
    • asMatrix.Rd
    • ...
    • t_sp.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • asMatrix.Rd
    • ...
    • t_sp.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; 62 lines (3%) are > 80 characters long.
  First few lines:
    • R/PRIOR_FUNCTIONS.R#L351 #' @return BB estimated size (1D optimi ...
    • ...
    • vignettes/bayNorm.Rmd#L372 - [2] <a href="https://www.biorxiv.org/c ...
ℹ NOTE: Consider 4 spaces instead of tabs; 7 lines (0%) contain tabs.
  First few lines:
    • vignettes/bayNorm.Rmd#L264 ...
    • ...
    • vignettes/bayNorm.Rmd#L295 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 82 lines (4%) are not.
  First few lines:
    • R/bayNorm.r#L130 ...
    • ...
    • vignettes/bayNorm.Rmd#L234 return(list(adjpval=adjpval, logFC_re= ...
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 bayNorm.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.