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r-software [2021/05/06 10:14] aorthr-software [2023/07/12 06:39] (current) aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 4.(4.0.5)+  * Version: 4.(4.3.1)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: May2021+  * Updated: July2023
   * Link: https://www.r-project.org/   * Link: https://www.r-project.org/
  
 ===== Usage ===== ===== Usage =====
  
-See versions of R that are available:+See which versions are available:
 <code>$ module avail R</code> <code>$ module avail R</code>
  
 Load one version into your environment and run it: Load one version into your environment and run it:
-<code>$ module load R/4.0+<code>$ module load R/4.3
 $ R</code> $ 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.+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/available_software/software_list/r#6|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:+First, compile the main R application:
  
 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://cran.r-project.org/src/base/R-4/R-4.0.5.tar.gz +$ wget https://cran.r-project.org/src/base/R-4/R-4.3.1.tar.gz 
-$ tar xf R-4.0.5.tar.gz +$ tar xf R-4.3.1.tar.gz 
-$ cd R-4.0.+$ cd R-4.3.1 
-# install packages to enable capabilities in R +$ sudo dnf install tcl-devel tk-devel 
-$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel glibc-headers pcre2-devel.x86_64 +$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.3 
-# install a newer compiler from Red Hat software collections +chrt -b 0 make -j4 
-$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ +$ sudo mv /export/apps/R/4.3 /export/apps/R/4.3.bak 
-$ scl enable devtoolset-7 bash +$ sudo mkdir /export/apps/R/4.3 
-# 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 aorth:aorth /export/apps/R/4.3 
-$ export CFLAGS='-std=gnu99 -g -O2' +$ make install</code>
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.0 +
-$ make -j4 +
-$ sudo mv /export/apps/R/4.0.3 +
-$ sudo mkdir -p /export/apps/R/4.0 +
-$ sudo chown aorth:aorth /export/apps/R/4.0 +
-$ make install +
-$ sudo rm -rf /export/apps/R/4.0.3</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: 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/apps/R/4.0/bin/R +<code>$ /export/apps/R/4.3/bin/R 
-> 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'))+# > Sys.setenv(MAKEFLAGS = "-j2") # didn't try 
 +> options(Ncpus = 4) # This does 4 parallel package installs 
 +> install.packages('sf', repo='https://cloud.r-project.org')
 > install.packages("hierfstat", repos="https://cran.r-project.org") > install.packages("hierfstat", repos="https://cran.r-project.org")
 > install.packages("adegenet", repos="https://cran.r-project.org") > install.packages("adegenet", repos="https://cran.r-project.org")
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 > install_github("lucidif/HiCeekR", repos=BiocManager::repositories()) > install_github("lucidif/HiCeekR", repos=BiocManager::repositories())
 > q() > q()
-$ sudo chown -R root:root /export/apps/R/4.0</code> +$ sudo chown -R root:root /export/apps/R/4.3</code>
- +
-**Note:** some of these packages will need system libraries installed, for example: +
-  * libgit2-devel.x86_64 +
-  * libjpeg-turbo-devel.x86_64 +
-  * gsl-devel.x86_64+
r-software.1620296057.txt.gz · Last modified: 2021/05/06 10:14 by aorth