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r-software [2017/04/24 13:06]
aorth [Usage]
r-software [2019/10/27 18:44] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Latest version: 3.3.3+  * Version: 3.6 (3.6.1)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: ​April2017 +  * Updated: ​October2019 
-  * 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>​
  
-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].+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 ​(also covers ​the installation of zlib, bzip2, xz, pcre, and curl, as they are needed by since ~3.3.x):+Notes from the sysadmin during installation
 + 
 +First, compile ​the main application with GCC 7 from Red Hat's ''​devtoolset-7''​ software collection:
  
 <​code>​$ cd /tmp <​code>​$ cd /tmp
-$ wget http://zlib.net/zlib-1.2.11.tar.xz +$ wget https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz 
-$ tar xf zlib-1.2.11.tar.xz +$ tar xf R-3.6.1.tar.gz 
-$ cd zlib-1.2.11 +$ cd R-3.6.
-$ ./configure --prefix=/​export/​apps/​zlib/1.2.11 +# install packages to enable capabilities in R 
-$ make +$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel 
-$ make check +# install a newer compiler from Red Hat software collections 
-$ sudo mkdir -p /​export/​apps/​zlib/1.2.11 +$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ 
-$ sudo chown aorth /​export/​apps/​zlib/1.2.11 +$ scl enable devtoolset-7 bash 
-$ make install +# R packages are written in C99 and GCC 7 uses a newer standard by default, so tell configure script to use C99 explicitly 
-$ sudo chown -R root:​root ​/export/​apps/​zlib/​1.2.11+$ export CFLAGS='​-std=gnu99 ​ -g -O2' 
 +$ ./​configure ​--enable-R-shlib ​--prefix=/​export/​apps/​R/3.6 
 +$ make -j4 
 +$ sudo mkdir -p /​export/​apps/​R/3.6 
 +$ sudo chown aorth:aorth /​export/​apps/​R/3.6 
 +$ make install</code>
  
-$ cd /tmp +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 http://​www.bzip.org/​1.0.6/​bzip2-1.0.6.tar.gz +
-$ tar xf bzip2-1.0.6.tar.gz +
-$ cd bzip2-1.0.6 +
-$ make -f Makefile-libbz2_so +
-$ sudo mkdir -p /​export/​apps/​bzip2/​1.0.6 +
-$ sudo chown aorth /​export/​apps/​bzip2/​1.0.6 +
-$ make install ​PREFIX=/​export/​apps/​bzip2/​1.0.6 +
-$ sudo chown -R root:root /​export/​apps/​bzip2/​1.0.6+
  
-cd /tmp +<​code>​export LD_LIBRARY_PATH=/​export/​apps/​gdal/2.4.2/lib 
-$ wget https://​tukaani.org/​xz/​xz-5.2.3.tar.xz +install.packages("​BiocManager",​ repos="​https://cran.r-project.org") 
-$ tar xf xz-5.2.3.tar.xz +> 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"​)) 
-$ cd xz-5.2.3 +> install.packages("​poppr",​ repos="​https://​cran.r-project.org") 
-$ ./configure --prefix=/​export/​apps/​xz/5.2.+> install.packages("​vcfR",​ repos="​https:​//cran.r-project.org")</​code>​
-$ make +
-$ make check +
-$ sudo mkdir -p /​export/​apps/​xz/​5.2.3 +
-$ sudo chown aorth /export/​apps/​xz/​5.2.3 +
-$ make install +
-$ sudo chown -R root:root /​export/​apps/​xz/​5.2.3 +
- +
-$ cd /tmp +
-$ wget http://downloads.sourceforge.net/​pcre/​pcre-8.40.tar.bz2 +
-$ tar xf pcre-8.40.tar.bz2 +
-$ cd pcre-8.40 +
-$ ./configure --prefix=/​export/​apps/​pcre/​8.40 --enable-unicode-properties --enable-pcre16 --enable-pcre32 --enable-pcregrep-libz --enable-pcregrep-libbz2 --enable-pcretest-libreadline +
-$ make +
-$ make check +
-$ sudo mkdir -p /​export/​apps/​pcre/​8.40 +
-$ sudo chown aorth /​export/​apps/​pcre/​8.40 +
-$ make install +
-$ sudo chown -R root:root /export/​apps/​pcre/8.40 +
- +
-$ cd /tmp +
-$ tar xf curl-7.54.0.tar.gz +
-$ cd curl-7.54.0 +
-$ ./configure ​--enable-ipv6 --prefix=/​export/​apps/​curl/​7.54.0 +
-$ make +
-$ make check +
-$ sudo mkdir -p /​export/​apps/​curl/​7.54.0 +
-$ sudo chown aorth /​export/​apps/​curl/​7.54.0 +
-$ make install +
-$ sudo chown -R root:root /​export/​apps/​curl/​7.54.0 +
- +
-$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/​export/​apps/​zlib/​1.2.11/​lib:/​export/​apps/​bzip2/​1.0.6/​lib:/​export/​apps/​xz/​5.2.3/​lib:/​export/​apps/​pcre/​8.40/​lib:/​export/​apps/​curl/​7.54.0/​lib LDFLAGS="$LDFLAGS ​-L/​export/​apps/​zlib/​1.2.11/​lib ​-L/​export/​apps/​bzip2/​1.0.6/​lib ​-L/​export/​apps/​xz/​5.2.3/​lib ​-L/​export/​apps/​pcre/​8.40/​lib -L/​export/​apps/​curl/​7.54.0/​lib"​ CFLAGS="​$CFLAGS -I/​export/​apps/​zlib/1.2.11/include -I/​export/​apps/​bzip2/​1.0.6/​include -I/​export/​apps/​xz/​5.2.3/include -I/export/​apps/​pcre/​8.40/​include ​-I/​export/​apps/​curl/​7.54.0/​include" +
-$ wget https://​cran.r-project.org/​src/​base/​R-3/​R-3.3.3.tar.gz +
-$ tar xf R-3.3.3.tar.gz +
-$ cd R-3.3.3 +
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.3.3 +
-$ make -j4 +
-$ make install +
-$ sudo mkdir -p /​export/​apps/​R/​3.3.3 +
-$ sudo chown aorth /​export/​apps/​R/​3.3.3 +
-$ sudo chown -R root:root /​export/​apps/​R/​3.3.3 +
-$ exit</​code>​+
r-software.1493028389.txt.gz · Last modified: 2017/04/24 13:06 by aorth