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r-software [2017/02/06 13:10] – joguyar-software [2019/08/08 20:49] – aorth
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 ===== Information ===== ===== Information =====
  
-  * Latest version: 3.3.2+  * Version: 3.6 (3.6.1)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: February, 2017 +  * Updated: August, 2019 
-  * Link: http://www.r-project.org/+  * Link: https://www.r-project.org/
  
 ===== Usage ===== ===== Usage =====
  
-=== See versions of R which are available === +See versions of R that are available: 
-<code>module avail R</code>+<code>$ module avail R</code> 
 + 
 +Load one version into your environment and run it: 
 +<code>$ module load R/3.6 
 +$ R</code> 
 + 
 +Here is a good resource on [[https://www.osc.edu/resources/getting_started/howto/howto_install_local_r_packages|installing R packages into user libraries]].
  
 ===== Installation ====== ===== Installation ======
-Notes from the sysadmin during installation:<code> +Notes from the sysadmin during installation.
-- install zlib/1.2.8, R/3.3.2 requires it +
-$ cd /tmp +
-$ wget -qO- "https://downloads.sourceforge.net/project/libpng/zlib/1.2.8/zlib-1.2.8.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Flibpng%2Ffiles%2Fzlib%2F1.2.8%2F&ts=1486285008&use_mirror=netix" | tar zvx +
-$ sudo mkdir -p /export/apps/zlib/1.2.8 +
-$ sudo chown -R joguya:joguya /export/apps/zlib/1.2.8 +
-$ scl enable devtoolset-2 bash +
-$ cd zlib-1.2.8/ +
-$ ./configure --prefix=/export/apps/zlib/1.2.8 +
-$ make -j4 +
-$ make install +
-$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/zlib/1.2.8/lib LDFLAGS="-L/export/apps/zlib/1.2.8/lib" CFLAGS="-I/export/apps/zlib/1.2.8/include"+
  
-- install bzip2/1.0.6 +First, compile the main R application with GCC 7 from Red Hat's ''devtoolset-7'' software collection:
-$ wget -qO- http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz | tar xzv +
-$ cd bzip2-1.0.6/ +
-$ sudo mkdir -p /export/apps/bzip/1.0.6 +
-$ sudo chown -R joguya:joguya /export/apps/bzip/1.0.6 +
-$ make -f Makefile-libbz2_so +
-$ make  clean +
-$ make +
-$ make -n install PREFIX=/export/apps/bzip/1.0.6/ +
-$ make install PREFIX=/export/apps/bzip/1.0.6/ +
-$ export PATH=/export/apps/bzip/1.0.6/bin:$PATH LD_LIBRARY_PATH=/export/apps/zlib/1.2.8/lib:/export/apps/bzip/1.0.6/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/zlib/1.2.8/lib -L/export/apps/bzip/1.0.6/lib/" CFLAGS="-I/export/apps/zlib/1.2.8/include -I/export/apps/bzip/1.0.6/include"+
  
-- install xz instead of liblzma +<code>$ cd /tmp 
-$ wget -qO- http://tukaani.org/xz/xz-5.2.2.tar.gz | tar xzv +$ wget https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz 
-$ cd xz-5.2.2/ +$ tar xf R-3.6.1.tar.gz 
-$ sudo mkdir -p /export/apps/xz/5.2.2 +$ cd R-3.6.1 
-$ sudo chown -R joguya:joguya /export/apps/xz/5.2.2 +# install packages to enable capabilities in R 
-$ ./configure --prefix=/export/apps/xz/5.2.2+$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel 
 +# install a newer compiler from Red Hat software collections 
 +$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ 
 +$ scl enable devtoolset-7 bash 
 +$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.6
 $ make -j4 $ make -j4
-$ make install +$ sudo mkdir -p /export/apps/R/3.6 
-$ export PATH=/export/apps/bzip/1.0.6/bin:/export/apps/xz/5.2.2/bin:$PATH LD_LIBRARY_PATH=/export/apps/zlib/1.2.8/lib:/export/apps/bzip/1.0.6/lib:/export/apps/xz/5.2.2/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/zlib/1.2.8/lib -L/export/apps/bzip/1.0.6/lib -L/export/apps/xz/5.2.2/lib" CFLAGS="-I/export/apps/zlib/1.2.8/include -I/export/apps/bzip/1.0.6/include -I/export/apps/xz/5.2.2/include"+$ sudo chown aorth /export/apps/R/3.6 
 +$ make install</code>
  
-- install pcre/8.35 +Then install some common libraries used by our users (to save space, overhead from tens of thousands of header and library files, and users's time):
-$ wget -qO- http://downloads.sourceforge.net/pcre/pcre-8.35.tar.bz2 | tar xjv +
-$ cd pcre-8.35/ +
-$ sudo mkdir -p /export/apps/pcre/8.35 +
-$ sudo chown -R joguya:joguya /export/apps/pcre/8.35 +
-$ ./configure --prefix=/export/apps/pcre/8.35 --enable-unicode-properties --enable-pcre16 --enable-pcre32 --enable-pcregrep-libz --enable-pcregrep-libbz2 --enable-pcretest-libreadline --enable-static +
-$ make -j4 +
-$ make check +
-$ make install +
-$ export PATH=/export/apps/bzip/1.0.6/bin:/export/apps/xz/5.2.2/bin:/export/apps/pcre/8.35/bin:$PATH LD_LIBRARY_PATH=/export/apps/zlib/1.2.8/lib:/export/apps/bzip/1.0.6/lib:/export/apps/xz/5.2.2/lib:/export/apps/pcre/8.35/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/zlib/1.2.8/lib -L/export/apps/bzip/1.0.6/lib -L/export/apps/xz/5.2.2/lib -L/export/apps/pcre/8.35/lib" CFLAGS="-I/export/apps/zlib/1.2.8/include -I/export/apps/bzip/1.0.6/include -I/export/apps/xz/5.2.2/include -I/export/apps/pcre/8.35/include"+
  
-- install libcurl/7.47 
-$ wget -qO- https://curl.haxx.se/download/curl-7.47.1.tar.gz | tar xvz 
-$ cd curl-7.47.1 
-$ sudo mkdir -p /export/apps/curl/7.47.1/ 
-$ sudo chown -R joguya:joguya /export/apps/curl/7.47.1/ 
-$ ./configure --prefix=/export/apps/curl/7.47.1 
-$ ./configure --enable-ipv6 --enable-ldap --enable-ldaps --with-nghttp2 --prefix=/export/apps/curl/7.47.1 
-$ export PATH=/export/apps/bzip/1.0.6/bin:/export/apps/xz/5.2.2/bin:/export/apps/pcre/8.35/bin:/export/apps/curl/7.47.1/bin:$PATH LD_LIBRARY_PATH=/export/apps/zlib/1.2.8/lib:/export/apps/bzip/1.0.6/lib:/export/apps/xz/5.2.2/lib:/export/apps/pcre/8.35/lib:/export/apps/curl/7.47.1/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/zlib/1.2.8/lib -L/export/apps/bzip/1.0.6/lib -L/export/apps/xz/5.2.2/lib -L/export/apps/pcre/8.35/lib -L/export/apps/curl/7.47.1/lib" CFLAGS="-I/export/apps/zlib/1.2.8/include -I/export/apps/bzip/1.0.6/include -I/export/apps/xz/5.2.2/include -I/export/apps/pcre/8.35/include -I/export/apps/curl/7.47.1/include" 
- 
-- install R/3.3.2 
-$ cd /tmp/ 
-$ wget -qO- https://cran.r-project.org/src/base/R-3/R-3.3.2.tar.gz | tar zxv 
-$ cd R-3.3.2/ 
-$ scl enable devtoolset-2 bash 
-$ sudo mkdir /export/apps/R/3.3.2 
-$ sudo chown -R joguya:joguya /export/apps/R/3.3.2 
-$ ./configure --enable-R-static-lib --prefix=/export/apps/R/3.3.2 
-$ make -j4 
-$ make install 
-$ sudo chown -R root:root /export/apps/R/3.3.2 
-</code> 
r-software.txt · Last modified: 2023/07/12 06:39 by aorth