Differences

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--- r-software [2017/04/24 10:06] – [Usage] aorth
+++ r-software [2021/01/25 12:39] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest version: 3.3.3
+  * Version: 4.0 (4.0.3)
   * Added: February, 2015
-  * Updated: April, 2017
+  * Updated: December, 2020
-  * Link: http://www.r-project.org/
+  * Link: https://www.r-project.org/
 ===== Usage =====
-=== See versions of R which are available ===
+See versions of R that are available:
-<code>module avail R</code>
+<code>$ module avail 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]].
+Load one version into your environment and run it:
+<code>$ module load R/4.0
+$ 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 ======
-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 with GCC 7 from Red Hat's ''devtoolset-7'' software collection:
 <code>$ cd /tmp
-$ wget http://zlib.net/zlib-1.2.11.tar.xz
+$ wget https://cran.r-project.org/src/base/R-4/R-4.0.3.tar.gz
-$ tar xf zlib-1.2.11.tar.xz
+$ cd R-4.0.3
-$ cd zlib-1.2.11
+# install packages to enable capabilities in R
-$ ./configure --prefix=/export/apps/zlib/1.2.11
+$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel glibc-headers pcre2-devel.x86_64
-$ make
+# install a newer compiler from Red Hat software collections
-$ make check
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
-$ sudo mkdir -p /export/apps/zlib/1.2.11
+$ scl enable devtoolset-7 bash
-$ sudo chown aorth /export/apps/zlib/1.2.11
+# R packages are written in C99 and GCC 7 uses a newer standard by default, so tell configure script to use C99 explicitly
-$ make install
+$ export CFLAGS='-std=gnu99 -g -O2'
-$ sudo chown -R root:root /export/apps/zlib/1.2.11
+$ ./configure --enable-R-shlib --prefix=/export/apps/R/4.0
+$ make -j4
+$ sudo mkdir -p /export/apps/R/4.0
+$ sudo chown aorth:aorth /export/apps/R/4.0
+$ make install</code>
-$ 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:
-$ 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
+<code>$ /export/apps/R/4.0/bin/R
-$ wget https://tukaani.org/xz/xz-5.2.3.tar.xz
+> 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'))
-$ tar xf xz-5.2.3.tar.xz
+> install.packages("hierfstat", repos="https://cran.r-project.org")
-$ cd xz-5.2.3
+> install.packages("adegenet", repos="https://cran.r-project.org")
-$ ./configure --prefix=/export/apps/xz/5.2.3
+> install.packages("BiocManager", repos="https://cran.r-project.org")
-$ make
+> install.packages("poppr", repos="https://cran.r-project.org")
-$ make check
+> install.packages("vcfR", repos="https://cran.r-project.org")
-$ sudo mkdir -p /export/apps/xz/5.2.3
+> q()
-$ sudo chown aorth /export/apps/xz/5.2.3
+$ sudo chown -R root:root /export/apps/R/4.0</code>
-$ make install
-$ sudo chown -R root:root /export/apps/xz/5.2.3
-$ cd /tmp
+**Note:** some of these packages will need system libraries installed, for example:
-$ wget http://downloads.sourceforge.net/pcre/pcre-8.40.tar.bz2
+  * libgit2-devel.x86_64
-$ tar xf pcre-8.40.tar.bz2
+  * libjpeg-turbo-devel.x86_64
-$ cd pcre-8.40
+  * gsl-devel.x86_64
-$ ./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
-$ 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="$CFLAGS -I/export/apps/zlib/1.2.11/include -I/export/apps/bzip2/1.0.6/include -I/export/apps/xz/5.2.3/include -I/export/apps/pcre/8.40/include -I/export/apps/curl/7.54.0/include"
-$ wget https://cran.r-project.org/src/base/R-3/R-3.3.3.tar.gz
-$ tar xf R-3.3.3.tar.gz
-$ cd R-3.3.3
-$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.3.3
-$ make -j4
-$ make install
-$ sudo mkdir -p /export/apps/R/3.3.3
-$ sudo chown aorth /export/apps/R/3.3.3
-$ sudo chown -R root:root /export/apps/R/3.3.3
-$ exit</code>