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

[noreply at r-forge.r-project.org]

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