ILRI Research Computing

User Tools

Site Tools

You are here: start » r-software
r-software

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
Last revisionBoth sides next revision
r-software [2017/02/06 13:10] – joguyar-software [2023/07/11 07:22] – aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Latest version: 3.3.2+  * Version: 4.3 (4.3.0)
   * Added: February, 2015   * Added: February, 2015
-  * Updated: February, 2017 +  * Updated: May, 2023 
-  * 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>
  
-===== Installation ====== +Load one version into your environment and run it: 
-Notes from the sysadmin during installation:<code> +<code>$ module load R/4.3 
-- install zlib/1.2.8, R/3.3.2 requires it +$ R</code>
-$ cd /tmp +
-$ wget -qO- "https://downloads.sourceforge.net/project/libpng/zlib/1.2.8/zlib-1.2.8.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Flibpng%2Ffiles%2Fzlib%2F1.2.8%2F&ts=1486285008&use_mirror=netix" | tar zvx +
-$ sudo mkdir -p /export/apps/zlib/1.2.8 +
-$ sudo chown -R joguya:joguya /export/apps/zlib/1.2.8 +
-$ scl enable devtoolset-2 bash +
-$ cd zlib-1.2.8/ +
-$ ./configure --prefix=/export/apps/zlib/1.2.8 +
-$ make -j4 +
-$ make install +
-$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/zlib/1.2.8/lib LDFLAGS="-L/export/apps/zlib/1.2.8/lib" CFLAGS="-I/export/apps/zlib/1.2.8/include"+
  
-- install bzip2/1.0.6 +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. 
-$ wget -qO- http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz | tar xzv + 
-$ cd bzip2-1.0.6/ +===== Installation ====== 
-$ sudo mkdir -p /export/apps/bzip/1.0.6 +Notes from the sysadmin during installation.
-$ sudo chown -R joguya:joguya /export/apps/bzip/1.0.6 +
-$ make -f Makefile-libbz2_so +
-$ make  clean +
-$ make +
-$ make -n install PREFIX=/export/apps/bzip/1.0.6/ +
-$ make install PREFIX=/export/apps/bzip/1.0.6/ +
-$ export PATH=/export/apps/bzip/1.0.6/bin:$PATH LD_LIBRARY_PATH=/export/apps/zlib/1.2.8/lib:/export/apps/bzip/1.0.6/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/zlib/1.2.8/lib -L/export/apps/bzip/1.0.6/lib/" CFLAGS="-I/export/apps/zlib/1.2.8/include -I/export/apps/bzip/1.0.6/include"+
  
-- install xz instead of liblzma +First, compile the main R application:
-$ wget -qO- http://tukaani.org/xz/xz-5.2.2.tar.gz | tar xzv +
-$ cd xz-5.2.2/ +
-$ sudo mkdir -p /export/apps/xz/5.2.2 +
-$ sudo chown -R joguya:joguya /export/apps/xz/5.2.2 +
-$ ./configure --prefix=/export/apps/xz/5.2.2 +
-$ make -j4 +
-$ make install +
-$ export PATH=/export/apps/bzip/1.0.6/bin:/export/apps/xz/5.2.2/bin:$PATH LD_LIBRARY_PATH=/export/apps/zlib/1.2.8/lib:/export/apps/bzip/1.0.6/lib:/export/apps/xz/5.2.2/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/zlib/1.2.8/lib -L/export/apps/bzip/1.0.6/lib -L/export/apps/xz/5.2.2/lib" CFLAGS="-I/export/apps/zlib/1.2.8/include -I/export/apps/bzip/1.0.6/include -I/export/apps/xz/5.2.2/include"+
  
-- install pcre/8.35 +<code>$ cd /tmp 
-$ wget -qO- http://downloads.sourceforge.net/pcre/pcre-8.35.tar.bz2 | tar xjv +$ wget https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz 
-$ cd pcre-8.35/ +$ tar xf R-4.3.0.tar.gz 
-$ sudo mkdir -p /export/apps/pcre/8.35 +$ cd R-4.3.0 
-$ sudo chown -R joguya:joguya /export/apps/pcre/8.35 +$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.3 
-$ ./configure --prefix=/export/apps/pcre/8.35 --enable-unicode-properties --enable-pcre16 --enable-pcre32 --enable-pcregrep-libz --enable-pcregrep-libbz2 --enable-pcretest-libreadline --enable-static +$ chrt -b 0 make -j4 
-$ make -j4 +$ sudo mkdir /export/apps/R/4.3 
-$ make check +$ sudo chown aorth:aorth /export/apps/R/4.3 
-$ make install +$ make install</code>
-$ export PATH=/export/apps/bzip/1.0.6/bin:/export/apps/xz/5.2.2/bin:/export/apps/pcre/8.35/bin:$PATH LD_LIBRARY_PATH=/export/apps/zlib/1.2.8/lib:/export/apps/bzip/1.0.6/lib:/export/apps/xz/5.2.2/lib:/export/apps/pcre/8.35/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/zlib/1.2.8/lib -L/export/apps/bzip/1.0.6/lib -L/export/apps/xz/5.2.2/lib -L/export/apps/pcre/8.35/lib" CFLAGS="-I/export/apps/zlib/1.2.8/include -I/export/apps/bzip/1.0.6/include -I/export/apps/xz/5.2.2/include -I/export/apps/pcre/8.35/include"+
  
-- install libcurl/7.47 +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:
-$ wget -qO- https://curl.haxx.se/download/curl-7.47.1.tar.gz | tar xvz +
-$ cd curl-7.47.1 +
-$ sudo mkdir -p /export/apps/curl/7.47.1/ +
-$ sudo chown -R joguya:joguya /export/apps/curl/7.47.1/ +
-$ ./configure --prefix=/export/apps/curl/7.47.1 +
-$ ./configure --enable-ipv6 --enable-ldap --enable-ldaps --with-nghttp2 --prefix=/export/apps/curl/7.47.1 +
-$ export PATH=/export/apps/bzip/1.0.6/bin:/export/apps/xz/5.2.2/bin:/export/apps/pcre/8.35/bin:/export/apps/curl/7.47.1/bin:$PATH LD_LIBRARY_PATH=/export/apps/zlib/1.2.8/lib:/export/apps/bzip/1.0.6/lib:/export/apps/xz/5.2.2/lib:/export/apps/pcre/8.35/lib:/export/apps/curl/7.47.1/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/zlib/1.2.8/lib -L/export/apps/bzip/1.0.6/lib -L/export/apps/xz/5.2.2/lib -L/export/apps/pcre/8.35/lib -L/export/apps/curl/7.47.1/lib" CFLAGS="-I/export/apps/zlib/1.2.8/include -I/export/apps/bzip/1.0.6/include -I/export/apps/xz/5.2.2/include -I/export/apps/pcre/8.35/include -I/export/apps/curl/7.47.1/include"+
  
-- install R/3.3.2 +<code>$ /export/apps/R/4.3/bin/R 
-$ cd /tmp/ +# > Sys.setenv(MAKEFLAGS = "-j2") # didn't try 
-$ wget -qO- https://cran.r-project.org/src/base/R-3/R-3.3.2.tar.gz | tar zxv +> options(Ncpus = 4) # This does 4 parallel package installs 
-$ cd R-3.3.2/ +> install.packages('sf', repo='https://cloud.r-project.org') 
-$ scl enable devtoolset-2 bash +> install.packages("hierfstat", repos="https://cran.r-project.org") 
-$ sudo mkdir /export/apps/R/3.3.2 +> install.packages("adegenet", repos="https://cran.r-project.org") 
-$ sudo chown -R joguya:joguya /export/apps/R/3.3.2 +> install.packages("BiocManager", repos="https://cran.r-project.org") 
-$ ./configure --enable-R-static-lib --prefix=/export/apps/R/3.3.2 +> install.packages("poppr", repos="https://cran.r-project.org") 
-$ make -j4 +> install.packages("vcfR", repos="https://cran.r-project.org") 
-$ make install +> install.packages("devtools", repos="https://cran.r-project.org") 
-$ sudo chown -R root:root /export/apps/R/3.3.2 +> library(devtools) 
-</code>+> install_github("HenrikBengtsson/TopDom") 
 +> install_github("lucidif/HiCeekR", repos=BiocManager::repositories()) 
 +> q() 
 +$ sudo chown -R root:root /export/apps/R/4.3</code>
r-software.txt · Last modified: 2023/07/12 06:39 by aorth