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r-software [2017/02/06 13:10] – joguyar-software [2020/05/12 13:38] – 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: October, 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> 
 + 
 +Use ''installed.packages()'' to check the list of packages installed in the ILRI environment by default. 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]] if you need other packages.
  
 ===== 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 glibc-headers 
 +# 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 
 +# R packages are written in C99 and GCC 7 uses a newer standard by default, so tell configure script to use C99 explicitly 
 +$ export CFLAGS='-std=gnu99  -g -O2' 
 +$ ./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:aorth /export/apps/R/3.6 
 +$ make install</code>
  
-- install pcre/8.35 +Then install some common libraries used by our users because some of them are quite complicated, and installing them globally saves tens of thousands of header files and libraries being installed into user libraries anyways:
-$ 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 +<code>$ export LD_LIBRARY_PATH=/export/apps/gdal/2.4.2/lib 
-$ wget -qO- https://curl.haxx.se/download/curl-7.47.1.tar.gz | tar xvz +> install.packages("BiocManager", repos="https://cran.r-project.org") 
-$ cd curl-7.47.1 +> install.packages("sf", repo="https://cloud.r-project.org", configure.args=c(sf = "--with-gdal-config=/export/apps/gdal/2.4.2/bin/gdal-config")) 
-$ sudo mkdir -p /export/apps/curl/7.47.1/ +> install.packages("poppr", repos="https://cran.r-project.org") 
-$ sudo chown -R joguya:joguya /export/apps/curl/7.47.1/ +> install.packages("vcfR", repos="https://cran.r-project.org")</code>
-$ ./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