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r-software [2017/04/24 10:06] – [Usage] aorthr-software [2022/05/27 06:32] – aorth
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 ===== Information ===== ===== Information =====
  
-  * Latest version: 3.3.3+  * Version: 4.2 (4.2.0)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: April, 2017 +  * Updated: May, 2022 
-  * Link: http://www.r-project.org/+  * Link: https://www.r-project.org/
  
 ===== Usage ===== ===== Usage =====
  
-=== See versions of R which are available === +See which versions are available: 
-<code>module avail R</code>+<code>$ module avail R</code>
  
-Here is a good resource on [installing R packages into user libraries|https://www.osc.edu/resources/getting_started/howto/howto_install_local_r_packages].+Load one version into your environment and run it: 
 +<code>$ module load R/4.2 
 +$ 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.
  
 ===== Installation ====== ===== Installation ======
-Notes from the sysadmin during installation (also covers the installation of zlib, bzip2, xz, pcre, and curl, as they are needed by R since ~3.3.x):+Notes from the sysadmin during installation. 
 + 
 +First, compile the main R application:
  
 <code>$ cd /tmp <code>$ cd /tmp
-$ wget http://zlib.net/zlib-1.2.11.tar.xz +$ wget https://cran.r-project.org/src/base/R-4/R-4.2.0.tar.gz 
-$ tar xf zlib-1.2.11.tar.xz +$ tar xf R-4.2.0.tar.gz  
-$ cd zlib-1.2.11 +$ cd R-4.2.0 
-$ ./configure --prefix=/export/apps/zlib/1.2.11 +$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.2 
-$ make +$ chrt -b 0 make -j4 
-$ make check +$ sudo mkdir /export/apps/R/4.2 
-$ sudo mkdir -p /export/apps/zlib/1.2.11 +$ sudo chown aorth:aorth /export/apps/R/4.2 
-$ sudo chown aorth /export/apps/zlib/1.2.11 +$ make install</code>
-$ make install +
-$ sudo chown -R root:root /export/apps/zlib/1.2.11 +
- +
-$ cd /tmp +
-$ wget http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz +
-$ tar xf bzip2-1.0.6.tar.gz +
-$ cd bzip2-1.0.6 +
-$ make -f Makefile-libbz2_so +
-$ sudo mkdir -p /export/apps/bzip2/1.0.6 +
-$ sudo chown aorth /export/apps/bzip2/1.0.6 +
-$ make install PREFIX=/export/apps/bzip2/1.0.6 +
-$ sudo chown -R root:root /export/apps/bzip2/1.0.6 +
- +
-$ cd /tmp +
-$ wget https://tukaani.org/xz/xz-5.2.3.tar.xz +
-$ tar xf xz-5.2.3.tar.xz +
-$ cd xz-5.2.3 +
-$ ./configure --prefix=/export/apps/xz/5.2.3 +
-$ make +
-$ make check +
-$ sudo mkdir -p /export/apps/xz/5.2.3 +
-$ sudo chown aorth /export/apps/xz/5.2.3 +
-$ make install +
-$ sudo chown -R root:root /export/apps/xz/5.2.3 +
- +
-$ cd /tmp +
-$ wget http://downloads.sourceforge.net/pcre/pcre-8.40.tar.bz2 +
-$ tar xf pcre-8.40.tar.bz2 +
-$ cd pcre-8.40 +
-$ ./configure --prefix=/export/apps/pcre/8.40 --enable-unicode-properties --enable-pcre16 --enable-pcre32 --enable-pcregrep-libz --enable-pcregrep-libbz2 --enable-pcretest-libreadline +
-$ make +
-$ make check +
-$ sudo mkdir -p /export/apps/pcre/8.40 +
-$ sudo chown aorth /export/apps/pcre/8.40 +
-$ make install +
-$ sudo chown -R root:root /export/apps/pcre/8.40+
  
-$ cd /tmp +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:
-$ tar xf curl-7.54.0.tar.gz +
-$ cd curl-7.54.0 +
-$ ./configure --enable-ipv6 --prefix=/export/apps/curl/7.54.0 +
-$ make +
-$ make check +
-$ sudo mkdir -p /export/apps/curl/7.54.0 +
-$ sudo chown aorth /export/apps/curl/7.54.0 +
-$ make install +
-$ sudo chown -R root:root /export/apps/curl/7.54.0+
  
-$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/zlib/1.2.11/lib:/export/apps/bzip2/1.0.6/lib:/export/apps/xz/5.2.3/lib:/export/apps/pcre/8.40/lib:/export/apps/curl/7.54.0/lib LDFLAGS="$LDFLAGS -L/export/apps/zlib/1.2.11/lib -L/export/apps/bzip2/1.0.6/lib -L/export/apps/xz/5.2.3/lib -L/export/apps/pcre/8.40/lib -L/export/apps/curl/7.54.0/lib" CFLAGS="$CFLAGS -I/export/apps/zlib/1.2.11/include -I/export/apps/bzip2/1.0.6/include -I/export/apps/xz/5.2.3/include -I/export/apps/pcre/8.40/include -I/export/apps/curl/7.54.0/include" +<code>$ /export/apps/R/4.2/bin/R 
-$ wget https://cran.r-project.org/src/base/R-3/R-3.3.3.tar.gz +# > Sys.setenv(MAKEFLAGS = "-j2") # didn't try 
-$ tar xf R-3.3.3.tar.gz +> options(Ncpus = 4) # This does 4 parallel package installs 
-$ cd R-3.3.3 +> install.packages('sf', repo='https://cloud.r-project.org') 
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.3.3 +> install.packages("hierfstat", repos="https://cran.r-project.org") 
-$ make -j4 +> install.packages("adegenet", repos="https://cran.r-project.org") 
-$ make install +> install.packages("BiocManager", repos="https://cran.r-project.org") 
-$ sudo mkdir -p /export/apps/R/3.3.3 +> install.packages("poppr", repos="https://cran.r-project.org") 
-$ sudo chown aorth /export/apps/R/3.3.3 +> install.packages("vcfR", repos="https://cran.r-project.org") 
-$ sudo chown -R root:root /export/apps/R/3.3.3 +> install.packages("devtools", repos="https://cran.r-project.org") 
-$ exit</code>+> library(devtools) 
 +> install_github("HenrikBengtsson/TopDom") 
 +> install_github("lucidif/HiCeekR", repos=BiocManager::repositories()) 
 +> q() 
 +$ sudo chown -R root:root /export/apps/R/4.2</code>
r-software.txt · Last modified: 2023/07/12 06:39 by aorth