ILRI Research Computing

User Tools

Site Tools

You are here: start » r-software
r-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
Next revisionBoth sides next revision
r-software [2017/02/06 13:10] – joguyar-software [2018/07/18 10:15] – aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Latest version: 3.3.2+  * Latest version: 3.5.1
   * Added: February, 2015   * Added: February, 2015
-  * Updated: February, 2017 +  * Updated: July, 2018 
-  * 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>
  
-===== Installation ====== +Load one version into your environment and run it: 
-Notes from the sysadmin during installation:<code> +<code>$ module load R/3.5.1 
-- install zlib/1.2.8, R/3.3.2 requires it +$ R</code>
-$ 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 +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]].
-$ 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 +===== Installation ====== 
-$ wget -qO- http://tukaani.org/xz/xz-5.2.2.tar.gz | tar xzv +Notes from the sysadmin during installation:
-$ cd xz-5.2.2/ +
-$ sudo mkdir -p /export/apps/xz/5.2.2 +
-$ sudo chown -R joguya:joguya /export/apps/xz/5.2.2 +
-$ ./configure --prefix=/export/apps/xz/5.2.2 +
-$ make -j4 +
-$ make install +
-$ 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" +
- +
-- install pcre/8.35 +
-$ 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 +<code>$ wget http://cran.mirror.ac.za/src/base/R-3/R-3.5.1.tar.gz 
-$ cd /tmp/ +$ tar xf R-3.5.1.tar.gz 
-$ wget -qO- https://cran.r-project.org/src/base/R-3/R-3.3.2.tar.gz | tar zxv +$ cd R-3.5.1 
-$ cd R-3.3.2/ +$ sudo yum install gcc-gfortran gcc-c++ libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel 
-$ scl enable devtoolset-2 bash +$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.5.1
-$ 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 -j4
 +$ sudo mkdir -p /export/apps/R/3.5.1
 +$ sudo chown aorth:aorth /export/apps/R/3.5.1
 $ make install $ make install
-$ sudo chown -R root:root /export/apps/R/3.3.2 +$ sudo chown -R root:root /export/apps/R/3.5.1</code>
-</code>+
r-software.txt · Last modified: 2023/07/12 06:39 by aorth