Differences

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--- r-software [2017/02/06 13:10] – joguya
+++ r-software [2017/04/28 08:38] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest version: 3.3.2
+  * Latest version: 3.3.3
   * Added: February, 2015
-  * Updated: February, 2017
+  * Updated: April, 2017
   * Link: http://www.r-project.org/
@@ Line 13: / Line 13: @@
 === See versions of R which are available ===
 <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]].
 ===== Installation ======
-Notes from the sysadmin during installation:<code>
+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):
-- install zlib/1.2.8, R/3.3.2 requires it
-$ cd /tmp
+<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
+$ wget http://zlib.net/zlib-1.2.11.tar.xz
-$ sudo mkdir -p /export/apps/zlib/1.2.8
+$ tar xf zlib-1.2.11.tar.xz
-$ sudo chown -R joguya:joguya /export/apps/zlib/1.2.8
+$ cd zlib-1.2.11
-$ scl enable devtoolset-2 bash
+$ ./configure --prefix=/export/apps/zlib/1.2.11
-$ cd zlib-1.2.8/
+$ make
-$ ./configure --prefix=/export/apps/zlib/1.2.8
+$ make check
-$ make -j4
+$ sudo mkdir -p /export/apps/zlib/1.2.11
+$ sudo chown aorth /export/apps/zlib/1.2.11
 $ make install
-$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/export/apps/zlib/1.2.8/lib LDFLAGS="-L/export/apps/zlib/1.2.8/lib" CFLAGS="-I/export/apps/zlib/1.2.8/include"
+$ sudo chown -R root:root /export/apps/zlib/1.2.11
-- install bzip2/1.0.6
+$ cd /tmp
-$ wget -qO- http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz | tar xzv
+$ wget http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
-$ cd bzip2-1.0.6/
+$ tar xf bzip2-1.0.6.tar.gz
-$ sudo mkdir -p /export/apps/bzip/1.0.6
+$ cd bzip2-1.0.6
-$ sudo chown -R joguya:joguya /export/apps/bzip/1.0.6
 $ make -f Makefile-libbz2_so
-$ make  clean
+$ sudo mkdir -p /export/apps/bzip2/1.0.6
-$ make
+$ sudo chown aorth /export/apps/bzip2/1.0.6
-$ make -n install PREFIX=/export/apps/bzip/1.0.6/
+$ make install PREFIX=/export/apps/bzip2/1.0.6
-$ make install PREFIX=/export/apps/bzip/1.0.6/
+$ sudo chown -R root:root /export/apps/bzip2/1.0.6
-$ 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
+$ cd /tmp
-$ wget -qO- http://tukaani.org/xz/xz-5.2.2.tar.gz | tar xzv
+$ wget https://tukaani.org/xz/xz-5.2.3.tar.xz
-$ cd xz-5.2.2/
+$ tar xf xz-5.2.3.tar.xz
-$ sudo mkdir -p /export/apps/xz/5.2.2
+$ cd xz-5.2.3
-$ sudo chown -R joguya:joguya /export/apps/xz/5.2.2
+$ ./configure --prefix=/export/apps/xz/5.2.3
-$ ./configure --prefix=/export/apps/xz/5.2.2
+$ make
-$ make -j4
+$ make check
+$ sudo mkdir -p /export/apps/xz/5.2.3
+$ sudo chown aorth /export/apps/xz/5.2.3
 $ 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"
+$ sudo chown -R root:root /export/apps/xz/5.2.3
-- install pcre/8.35
+$ cd /tmp
-$ wget -qO- http://downloads.sourceforge.net/pcre/pcre-8.35.tar.bz2 | tar xjv
+$ wget http://downloads.sourceforge.net/pcre/pcre-8.40.tar.bz2
-$ cd pcre-8.35/
+$ tar xf pcre-8.40.tar.bz2
-$ sudo mkdir -p /export/apps/pcre/8.35
+$ cd pcre-8.40
-$ sudo chown -R joguya:joguya /export/apps/pcre/8.35
+$ ./configure --prefix=/export/apps/pcre/8.40 --enable-unicode-properties --enable-pcre16 --enable-pcre32 --enable-pcregrep-libz --enable-pcregrep-libbz2 --enable-pcretest-libreadline
-$ ./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
+$ make
-$ make -j4
 $ make check
+$ sudo mkdir -p /export/apps/pcre/8.40
+$ sudo chown aorth /export/apps/pcre/8.40
 $ make install
-$ 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"
+$ sudo chown -R root:root /export/apps/pcre/8.40
-- install libcurl/7.47
+$ cd /tmp
-$ wget -qO- https://curl.haxx.se/download/curl-7.47.1.tar.gz | tar xvz
+$ wget https://curl.haxx.se/download/curl-7.54.0.tar.gz
-$ cd curl-7.47.1
+$ tar xf curl-7.54.0.tar.gz
-$ sudo mkdir -p /export/apps/curl/7.47.1/
+$ cd curl-7.54.0
-$ sudo chown -R joguya:joguya /export/apps/curl/7.47.1/
+$ ./configure --enable-ipv6 --prefix=/export/apps/curl/7.54.0
-$ ./configure --prefix=/export/apps/curl/7.47.1
+$ make
-$ ./configure --enable-ipv6 --enable-ldap --enable-ldaps --with-nghttp2 --prefix=/export/apps/curl/7.47.1
+$ make check
-$ 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"
+$ 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
-- install R/3.3.2
+$ 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="$CFLAGS -I/export/apps/zlib/1.2.11/include -I/export/apps/bzip2/1.0.6/include -I/export/apps/xz/5.2.3/include -I/export/apps/pcre/8.40/include -I/export/apps/curl/7.54.0/include"
-$ cd /tmp/
+$ wget https://cran.r-project.org/src/base/R-3/R-3.3.3.tar.gz
-$ wget -qO- https://cran.r-project.org/src/base/R-3/R-3.3.2.tar.gz | tar zxv
+$ tar xf R-3.3.3.tar.gz
-$ cd R-3.3.2/
+$ cd R-3.3.3
-$ scl enable devtoolset-2 bash
+$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.3.3
-$ sudo mkdir /export/apps/R/3.3.2
-$ sudo chown -R joguya:joguya /export/apps/R/3.3.2
-$ ./configure --enable-R-static-lib --prefix=/export/apps/R/3.3.2
 $ make -j4
 $ make install
-$ sudo chown -R root:root /export/apps/R/3.3.2
+$ sudo mkdir -p /export/apps/R/3.3.3
-</code>
+$ sudo chown aorth /export/apps/R/3.3.3
+$ sudo chown -R root:root /export/apps/R/3.3.3
+$ exit</code>