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r-software [2019/08/08 20:01]
aorth
r-software [2020/05/12 13:38]
aorth
Line 6: Line 6:
   * Version: 3.6 (3.6.1)   * Version: 3.6 (3.6.1)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: August, 2019+  * Updated: October, 2019
   * Link: https://www.r-project.org/   * Link: https://www.r-project.org/
  
Line 18: Line 18:
 $ 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 ======
Line 30: Line 30:
 $ cd R-3.6.1 $ cd R-3.6.1
 # install packages to enable capabilities in R # install packages to enable capabilities in R
-$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel+$ 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 # 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++ $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
 $ scl enable devtoolset-7 bash $ 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 $ ./configure --enable-R-shlib --prefix=/export/apps/R/3.6
 $ make -j4 $ make -j4
 $ sudo mkdir -p /export/apps/R/3.6 $ sudo mkdir -p /export/apps/R/3.6
-$ sudo chown aorth /export/apps/R/3.6+$ sudo chown aorth:aorth /export/apps/R/3.6
 $ make install</code> $ make install</code>
  
-Then install some common libraries used by our users (to save space and time):+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:
  
 +<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.txt · Last modified: 2020/05/12 18:20 by aorth