[GenABEL-dev] [Genabel-commits] r1498 - pkg/GenABEL-general/scripts tutorials/GenABEL_general

[L.C. Karssen]

Hi Maksim,

Cool! That's a quick implementation!


Thanks,

Lennart.

On 20-12-13 09:22, noreply at r-forge.r-project.org wrote:
> Author: maksim
> Date: 2013-12-20 09:22:09 +0100 (Fri, 20 Dec 2013)
> New Revision: 1498
> 
> Modified:
>    pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
>    tutorials/GenABEL_general/Makefile
> Log:
> Added instructions which reduce size of GenABEL-tutorial.pdf while runing Makfilein from GenABEL_general. Rewrote part for installation fresh R packages.
> 
> Modified: pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh
> ===================================================================
> --- pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-20 06:28:26 UTC (rev 1497)
> +++ pkg/GenABEL-general/scripts/makedistrib_GenABEL.sh	2013-12-20 08:22:09 UTC (rev 1498)
> @@ -24,24 +24,28 @@
>  
>  
>  echo
> -echo Install the freshest R packages from CRAN repository...
> +echo Install the freshest R packages from CRAN and Bioconductor repository...
>  
> -echo "install.packages(\"roxygen2\", repos='http://cran.xl-mirror.nl')" > install_fresh_R_packages.R
> -echo "install.packages(\"mvtnorm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"methods\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"MASS\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"utils\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo
> -echo An R package qvalue is being installed from Bioconductor...
> -#echo "install.packages(\"qvalue\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "source(\"http://bioconductor.org/biocLite.R\")" >> install_fresh_R_packages.R
> -echo "biocLite(\"qvalue\")" >> install_fresh_R_packages.R
> -echo "install.packages(\"genetics\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"haplo.stats\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"hglm\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"PredictABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"VariABEL\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> -echo "install.packages(\"bigRR\", repos='http://cran.xl-mirror.nl')" >> install_fresh_R_packages.R
> +CRAN_repo="\"http://cran.xl-mirror.nl\""
> +
> +cat <<EOF > install_fresh_R_packages.R
> +install.packages("roxygen2", repos=$CRAN_repo) 
> +install.packages("mvtnorm", repos=$CRAN_repo) 
> +install.packages("methods", repos=$CRAN_repo) 
> +install.packages("MASS", repos=$CRAN_repo) 
> +install.packages("utils", repos=$CRAN_repo) 
> +
> +source("http://bioconductor.org/biocLite.R") 
> +biocLite("qvalue") 
> +
> +install.packages("genetics", repos=$CRAN_repo) 
> +install.packages("haplo.stats", repos=$CRAN_repo) 
> +install.packages("hglm", repos=$CRAN_repo) 
> +install.packages("PredictABEL", repos=$CRAN_repo) 
> +install.packages("VariABEL", repos=$CRAN_repo) 
> +install.packages("bigRR", repos=$CRAN_repo) 
> +EOF
> +
>  R -f install_fresh_R_packages.R
>  rm -rf install_fresh_R_packages.R
>  
> @@ -124,9 +128,11 @@
>  
>  if [ -f GenABEL_general/GenABEL-tutorial.pdf ];
>  then
> -cp GenABEL_general/GenABEL-tutorial.pdf GenABEL/inst/doc/.
> -echo
> -echo Build the working version of GenABEL...
> +#echo Compressing GenABEL_general/GenABEL-tutorial.pdf...
> +#gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen -dNOPAUSE -dQUIET -dBATCH -sOutputFile=GenABEL_general/GenABEL-tutorial.pdf_compressed GenABEL_general/GenABEL-tutorial.pdf
> +#echo Copying GenABEL_general/GenABEL-tutorial.pdf in GenABEL/inst/doc/...
> +cp GenABEL_general/GenABEL-tutorial.pdf GenABEL/inst/doc/
> +echo Buildngd the GenABEL...
>  R CMD build GenABEL
>  mkdir GenABEL_DISTRIBUTIVE_IS_HERE
>  cp GenABEL_*gz GenABEL_DISTRIBUTIVE_IS_HERE
> 
> Modified: tutorials/GenABEL_general/Makefile
> ===================================================================
> --- tutorials/GenABEL_general/Makefile	2013-12-20 06:28:26 UTC (rev 1497)
> +++ tutorials/GenABEL_general/Makefile	2013-12-20 08:22:09 UTC (rev 1498)
> @@ -22,6 +22,8 @@
>  	makeindex $<
>  	pdflatex $<
>  	pdflatex $<
> +	gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dNOPAUSE -dQUIET -dBATCH -sOutputFile=$(MAIN).pdf_compressed $(MAIN).pdf
> +	mv $(MAIN).pdf_compressed $(MAIN).pdf
>  
>  html: all
>  	mk4ht htlatex GenABEL-tutorial.tex myxhtml
> 
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-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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