User Tools

Site Tools


r-software

Differences

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

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
r-software [2019/08/08 20:01]
aorth
r-software [2019/10/27 15:41]
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 34: Line 34:
 $ 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