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r-software [2022/05/18 07:41] aorthr-software [2022/05/27 06:32] aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 4.(4.0.5)+  * Version: 4.(4.2.0)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: May, 2021+  * Updated: May, 2022
   * Link: https://www.r-project.org/   * Link: https://www.r-project.org/
  
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 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/4.2
 $ R</code> $ R</code>
  
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 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-4.2.0.tar.gz 
-$ tar xf R-4.0.5.tar.gz +$ tar xf R-4.2.0.tar.gz  
-$ cd R-4.0.5 +$ cd R-4.2.0 
-# install packages to enable capabilities in R +$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.2 
-$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel glibc-headers pcre2-devel.x86_64 +chrt -b 0 make -j4 
-# install a newer compiler from Red Hat software collections +$ sudo mkdir /export/apps/R/4.2 
-$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ +$ sudo chown aorth:aorth /export/apps/R/4.2 
-$ scl enable devtoolset-7 bash +$ make install</code>
-# 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/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/4.2/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")
Line 58: Line 51:
 > 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/4.2</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.txt · Last modified: 2023/07/12 06:39 by aorth