Differences

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--- documentation:r_setup [2015/04/07 01:49] – schuemie
+++ documentation:r_setup [2016/07/06 21:37] (current) – vojtechhuser
@@ Line 7: / Line 7: @@
 Here are instructions for when you just want to run the OHDSI tools.
-** Windows **
+==== Windows  ====
   - Install R, which you can download from [[http://cran.r-project.org/bin/windows/base/|CRAN]]. **Important**: it is best to install R in the root of your drive, so preferably in //c:/R/R-3.x.x//
@@ Line 16: / Line 17: @@
             * R_LIBRARY with the location of your R library (e.g. //c:/users/john/R/win-library/3.1//)
   - We found it is best to restart your computer for the environmental variables to take effect.
-  - Several OHDSI packages require [[http://www.java.com|Java]], so please install that as well.
+  - Several OHDSI packages require [[http://www.java.com|Java]], so please install that as well. On a 64-bit machine it is better to install the JDK rather than the JRE, since the JRE only seems to include the 32-bit version. If you have further trouble, be sure on Windows that your Path variable includes the path to jvm.dll (Windows Button --> type "path" --> Edit Environmental Variables --> Edit PATH variable, add to end ;C:/Program Files/Java/jre/bin/server) or wherever it is on your system.
+  - additional user notes (2016-07-06, Vojtech Huser). After many attempts to resolve the jml.dll issue, I was able to solve the error by forcing R to not try to install the package for all architectures. If all is failing, try adding install opts like this //install.packages("SqlRender",INSTALL_opts="--no-multiarch")//
+==== Ubuntu ====
+=== Install Java ===
+First, we completely remove openjdk if present:
+<code>
+sudo apt-get purge openjdk-\*
+</code>
+Next we install Oracle Java:
+<code>
+sudo apt-get install python-software-properties
+sudo add-apt-repository ppa:webupd8team/java
+sudo apt-get update
+sudo apt-get install oracle-java8-installer
+</code>
+=== Install Git ===
+<code>
+sudo apt-get install git-all
+</code>
+=== Install R ===
+<code>
+sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list'
+sudo gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
+sudo gpg -a --export E084DAB9 | sudo apt-key add -
+sudo apt-get update
+sudo apt-get install r-base
+sudo R CMD javareconf
+</code>
+If you're having trouble finding libjvm.so in R:
+<code>
+sudo updatedb
+locate libjvm.so
+sudo ln -s  /usr/lib/jvm/java-8-oracle/jre/lib/amd64/server/libjvm.so /usr/lib/
+</code>
+(adapt last line to correct location for your JRE)
+=== Install required Linux packages ===
+These libraries are required by some packages in R:
+<code>
+sudo apt-get install libcurl4-openssl-dev
+sudo apt-get install libssl-dev
+sudo apt-get install libxml2-dev
+sudo apt-get install liblzma-dev
+</code>
 ===== Tool developers =====