Package: CopyNumberPlots

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CopyNumberPlots.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CopyNumberPlots_1.0.1.tar.gz

StartedAt: 2019-10-16 02:54:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:01:06 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 367.9 seconds

RetCode: 0

Status:  OK

CheckDir: CopyNumberPlots.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CopyNumberPlots.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CopyNumberPlots_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CopyNumberPlots.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CopyNumberPlots/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CopyNumberPlots' version '1.0.1'
* 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 'CopyNumberPlots' 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 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
* 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 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CopyNumberPlots_1.0.1.tar.gz && rm -rf CopyNumberPlots.buildbin-libdir && mkdir CopyNumberPlots.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CopyNumberPlots.buildbin-libdir CopyNumberPlots_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CopyNumberPlots_1.0.1.zip && rm CopyNumberPlots_1.0.1.tar.gz CopyNumberPlots_1.0.1.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100  177k  100  177k    0     0  2577k      0 --:--:-- --:--:-- --:--:-- 2868k

install for i386

* installing *source* package 'CopyNumberPlots' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CopyNumberPlots'
    finding HTML links ... done
    EnsemblStyle                            html  
    UCSCStyle                               html  
    colByCopyNumber                         html  
    getBAFColumn                            html  
    getChrColumn                            html  
    getColumn                               html  
    getCopyNumberColors                     html  
    getCopyNumberColumn                     html  
    getEndColumn                            html  
    getIDColumn                             html  
    getLOHColumn                            html  
    getLRRColumn                            html  
    getPosColumn                            html  
    getSegmentValueColumn                   html  
    getStartColumn                          html  
    loadCopyNumberCalls                     html  
    loadCopyNumberCallsCNVkit               html  
    loadCopyNumberCallsCnmops               html  
    loadCopyNumberCallsDECoN                html  
    loadCopyNumberCallsDNAcopy              html  
    loadCopyNumberCallsPanelcnmops          html  
    loadCopyNumberCallsSeg                  html  
    loadCopyNumberCallspennCNV              html  
    loadSNPData                             html  
    loadSNPDataDNAcopy                      html  
    loadSNPDataFromVCF                      html  
    plotBAF                                 html  
    finding level-2 HTML links ... done

    plotCopyNumberCalls                     html  
    plotCopyNumberCallsAsLines              html  
    plotCopyNumberSummary                   html  
    plotLRR                                 html  
    prepareLabels                           html  
    removeNAs                               html  
    transformChr                            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

install for x64

* installing *source* package 'CopyNumberPlots' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CopyNumberPlots' as CopyNumberPlots_1.0.1.zip
* DONE (CopyNumberPlots)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CopyNumberPlots' successfully unpacked and MD5 sums checked