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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Clonality.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Clonality_1.43.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Clonality.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Clonality/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clonality' version '1.43.0'
* 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 'Clonality' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... NOTE
Foreign function call to a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
get.mutation.frequencies: no visible binding for global variable
  'freqdata'
Undefined global functions or variables:
  freqdata
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
clonality.analysis  38.92   0.28   39.21
LRtesting3or4tumors 14.76   0.03   14.79
LOHclonality         6.11   0.31    6.43
ECMtesting           5.57   0.00    5.56
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/Clonality.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Clonality
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Clonality' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Clonality'
    finding HTML links ... done
    Clonality-internal                      html  
    Clonality-package                       html  
    ECMtesting                              html  
    LOHclonality                            html  
    LRtesting3or4tumors                     html  
    SNVtest                                 html  
    SNVtest2                                html  
    ave.adj.probes                          html  
    chromosomePlots                         html  
    clonEM                                  html  
    clonality.analysis                      html  
    create.mutation.matrix                  html  
    freqdata                                html  
    genomewidePlots                         html  
    get.mutation.frequencies                html  
    grid.lik                                html  
    histogramPlot                           html  
    lcis                                    html  
    model.lik                               html  
    mutation.proba                          html  
    mutation.rem                            html  
    print.mutation.proba                    html  
    print.mutation.rem                      html  
    splitChromosomes                        html  
    xidens                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Clonality)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'switchBox' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'tximport' is missing or broken
 done