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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SARC.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SARC_1.4.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SARC.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SARC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SARC' version '1.4.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 whether package 'SARC' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
addExonsGenes: no visible global function definition for 'metadata'
addExonsGenes: no visible global function definition for 'metadata<-'
anovaOnCNV: no visible global function definition for 'metadata'
anovaOnCNV: no visible global function definition for 'metadata<-'
cnvConfidence: no visible global function definition for 'metadata'
cnvConfidence: no visible global function definition for 'metadata<-'
pasteExonsGenes: no visible global function definition for 'metadata'
pasteExonsGenes: no visible global function definition for 'metadata<-'
phDunnetonCNV: no visible global function definition for 'metadata'
phDunnetonCNV: no visible global function definition for 'metadata<-'
plotCovPrep: no visible global function definition for 'metadata'
plotCovPrep: no visible global function definition for 'metadata<-'
prepAnova: no visible global function definition for 'metadata'
prepAnova: no visible global function definition for 'metadata<-'
regionGrangeMake: no visible global function definition for 'metadata'
regionGrangeMake: no visible global function definition for
  'metadata<-'
regionMean: no visible global function definition for 'metadata'
regionMean: no visible global function definition for 'metadata<-'
regionQuantiles: no visible global function definition for 'metadata'
regionQuantiles: no visible global function definition for 'metadata<-'
regionSet: no visible global function definition for 'sortSeqlevels'
regionSet: no visible global function definition for 'metadata'
regionSet: no visible global function definition for 'metadata<-'
regionSplit: no visible global function definition for 'metadata'
regionSplit: no visible global function definition for 'metadata<-'
setQDplot: no visible global function definition for 'metadata'
setQDplot: no visible global function definition for 'metadata<-'
setupCNVplot: no visible global function definition for 'metadata'
setupCNVplot: no visible global function definition for 'metadata<-'
Undefined global functions or variables:
  metadata metadata<- sortSeqlevels
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
addExonsGenes   34.89   1.33   36.53
setupCNVplot    26.79   1.00   27.76
plotCNV         24.64   1.12   25.76
pasteExonsGenes 24.87   0.88   25.74
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/SARC.Rcheck/00check.log'
for details.