documentation:r_setup
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documentation:r_setup [2015/04/07 01:49] schuemie |
documentation:r_setup [2016/07/06 21:37] vojtechhuser |
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| Here are instructions for when you just want to run the OHDSI tools. | 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// | - 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// | ||
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| * R_LIBRARY with the location of your R library (e.g. //c:/users/john/R/win-library/3.1//) | * 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. | - 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 ===== | ===== Tool developers ===== | ||
documentation/r_setup.txt · Last modified: 2016/07/06 21:37 by vojtechhuser
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