Package: Clonality

Version: 1.26.0

Command: rm -rf Clonality.buildbin-libdir Clonality.Rcheck && mkdir Clonality.buildbin-libdir Clonality.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clonality.buildbin-libdir Clonality_1.26.0.tar.gz >Clonality.Rcheck\00install.out 2>&1 && cp Clonality.Rcheck\00install.out Clonality-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Clonality.buildbin-libdir --install="check:Clonality-install.out" --force-multiarch --no-vignettes --timings Clonality_1.26.0.tar.gz

StartedAt: 2018-04-11 22:58:05 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:02:06 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 240.8 seconds

RetCode: 0

Status:  OK

CheckDir: Clonality.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf Clonality.buildbin-libdir Clonality.Rcheck && mkdir Clonality.buildbin-libdir Clonality.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clonality.buildbin-libdir Clonality_1.26.0.tar.gz >Clonality.Rcheck\00install.out 2>&1 && cp Clonality.Rcheck\00install.out Clonality-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Clonality.buildbin-libdir --install="check:Clonality-install.out" --force-multiarch --no-vignettes --timings Clonality_1.26.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Clonality.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.26.0'
* 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 ... 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
clonality.analysis  57.77   0.13   57.89
LRtesting3or4tumors 18.10   0.00   18.10
LOHclonality         6.81   0.00    6.81
ECMtesting           5.25   0.00    5.25
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
clonality.analysis  66.23   0.16   66.44
LRtesting3or4tumors 21.34   0.00   21.34
ECMtesting           9.28   0.00    9.28
LOHclonality         8.01   0.00    8.01
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Clonality.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'Clonality' ...
** R
** data
** inst
** preparing 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  
    ave.adj.probes                          html  
    chromosomePlots                         html  
    clonality.analysis                      html  
    genomewidePlots                         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
In R CMD INSTALL

install for x64

* installing *source* package 'Clonality' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Clonality' as Clonality_1.26.0.zip
* DONE (Clonality)
In R CMD INSTALL
In R CMD INSTALL