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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings canceR_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/canceR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘canceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘canceR’ version ‘1.41.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘canceR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in Rd file 'dialogSpecificMut.Rd':
  ‘getSpecificMut’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in Rd file 'cbind.na.Rd':
  ‘cbind.na’

S3 methods shown with full name in Rd file 'rbind.na.Rd':
  ‘rbind.na’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'GSEA.EnrichmentScore.Rd':
  ‘gene.list’ ‘gene.set’ ‘weighted.score.type’ ‘correl.vector’
Argument items with no description in Rd file 'GSEA.EnrichmentScore2.Rd':
  ‘gene.list’ ‘gene.set’ ‘weighted.score.type’ ‘correl.vector’
Argument items with no description in Rd file 'GSEA.Gct2Frame.Rd':
  ‘filename’
Argument items with no description in Rd file 'GSEA.Gct2Frame2.Rd':
  ‘filename’
Argument items with no description in Rd file 'GSEA.GeneRanking.Rd':
  ‘A’ ‘class.labels’ ‘gene.labels’ ‘nperm’ ‘permutation.type’
  ‘sigma.correction’ ‘fraction’ ‘replace’ ‘reverse.sign’
Argument items with no description in Rd file 'GSEA.NormalizeCols.Rd':
  ‘V’
Argument items with no description in Rd file 'GSEA.NormalizeRows.Rd':
  ‘V’
Argument items with no description in Rd file 'GSEA.ReadClsFile.Rd':
  ‘file’
Argument items with no description in Rd file 'GSEA.Res2Frame.Rd':
  ‘filename’
Argument items with no description in Rd file 'GSEA.Threshold.Rd':
  ‘V’ ‘thres’ ‘ceil’
Argument items with no description in Rd file 'GSEA.VarFilter.Rd':
  ‘V’ ‘fold’ ‘delta’ ‘gene.names’
Argument items with no description in Rd file 'GSEA.write.gct.Rd':
  ‘gct’ ‘filename’
Argument items with no description in Rd file 'OLD.GSEA.EnrichmentScore.Rd':
  ‘gene.list’ ‘gene.set’
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/canceR.Rcheck/00check.log’
for details.