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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MIRit_1.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MIRit ────────────────────────────────────────────────────────────
✔ Package installed successfully
── MIRit session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRDh3GQ/fileda1ea7931c0a0/MIRit
→ BiocVersion: 3.24
→ Package: MIRit
→ PackageVersion: 1.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MIRit.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpRDh3GQ/fileda1ea7931c0a0/MIRit
→ installDir: /tmp/RtmpRDh3GQ/fileda1eaa8eed93
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MIRit ──────────────────────────────────────────────────
* 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 4.4.0 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (48%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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:
    • MIRit.Rmd
* Checking package installation calls in R code...
* Checking for library/require of MIRit...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/integration.R (line 481, column 19)
    • R/integration.R (line 482, column 25)
    • R/integration.R (line 613, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/association.R (line 45, column 13)
    • ...
    • R/visualization.R (line 3437, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/integration.R (line 900, column 24)
  • ...
  • suppressMessages() in R/topological-integration.R (line 653, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 46
functions greater than 50 lines.
  The longest 5 functions are:
    • plotCorrelation() (R/visualization.R): 436 lines
    • ...
    • plotDimensions() (R/visualization.R): 292 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • deAnalysis.Rd
  • ...
  • topologicalAnalysis.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 19% of man
pages use at least one of these tags.
  Found in files:
    • deAnalysis.Rd
    • ...
    • topologicalAnalysis.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test-association.R
test-differential-expression.R test-targets.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 10 lines (0%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L191 #' See [`MultiAssayExperiment-class`][Mu ...
    • ...
    • vignettes/MIRit.Rmd#L949 ```{r corPlot, fig.wide=TRUE, fig.cap="C ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 114 lines (1%) are
not.
  First few lines:
    • R/batch-correction.R#L294 function(x) ...
    • ...
    • vignettes/MIRit.Rmd#L1000 p = \frac{(a + b)!\ (c + d)!\ (a + c)! ...
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 MIRit.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.