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r-software [2019/08/08 23:01]
aorth
r-software [2019/10/27 18:44] (current)
aorth
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   * 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/​
  
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 $ 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 ======
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 $ 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.1565294461.txt.gz · Last modified: 2019/08/08 23:01 by aorth