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r-software [2019/01/28 20:52]
aorth
r-software [2019/10/27 18:44] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 3.5.2+  * Version: 3.6 (3.6.1)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: ​January, 2019+  * Updated: ​October, 2019
   * Link: https://​www.r-project.org/​   * Link: https://​www.r-project.org/​
  
Line 15: Line 15:
  
 Load one version into your environment and run it: Load one version into your environment and run it:
-<​code>​$ module load R/3.5+<​code>​$ module load R/3.6
 $ R</​code>​ $ 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]].+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:​+Notes from the sysadmin during installation
 + 
 +First, compile the main R application with GCC 7 from Red Hat's ''​devtoolset-7''​ software collection:
  
 <​code>​$ cd /tmp <​code>​$ cd /tmp
-$ wget https://​cran.r-project.org/​src/​base/​R-3/​R-3.5.2.tar.gz +$ wget https://​cran.r-project.org/​src/​base/​R-3/​R-3.6.1.tar.gz 
-$ tar xf R-3.5.2.tar.gz +$ tar xf R-3.6.1.tar.gz 
-$ cd R-3.5.2 +$ cd R-3.6.
-$ sudo yum install ​gcc-gfortran gcc-c++ ​libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel +# install packages to enable capabilities in R 
-$ ./configure --enable-R-shlib --prefix=/​export/​apps/​R/​3.5+$ 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 
 +# 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
-$ sudo mkdir -p /​export/​apps/​R/​3.5 +$ sudo mkdir -p /​export/​apps/​R/​3.6 
-$ sudo chown aorth:aorth /​export/​apps/​R/​3.5 +$ sudo chown aorth:aorth /​export/​apps/​R/​3.6 
-$ make install +$ make install</​code>​ 
-$ sudo chown -R root:root /​export/​apps/​R/​3.5 + 
-$ sudo yum remove gcc-c++ libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel</​code>​+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:
  
-Note to future Alandon't remove ''​gcc-gfortran''​ after the install ​because some users need it!+<​code>​$ export LD_LIBRARY_PATH=/​export/​apps/​gdal/​2.4.2/​lib 
 +> install.packages("​BiocManager",​ repos="​https://cran.r-project.org"​) 
 +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"​)) 
 +> install.packages("​poppr",​ repos="​https://​cran.r-project.org"​) 
 +> install.packages("​vcfR",​ repos="​https://​cran.r-project.org"​)</​code>​
r-software.1548697923.txt.gz · Last modified: 2019/01/28 20:52 by aorth