R - Revision history

Rf: up

2017-02-07T15:18:21Z

Rf: up

2017-02-07T14:44:21Z

Rf at 14:28, 7 February 2017

2017-02-07T14:28:49Z

Rf at 14:19, 7 February 2017

2017-02-07T14:19:52Z

Rf at 12:30, 7 February 2017

2017-02-07T12:30:46Z

Rf at 12:24, 7 February 2017

2017-02-07T12:24:08Z

Rf at 11:50, 7 February 2017

2017-02-07T11:50:42Z

Rf at 11:43, 7 February 2017

2017-02-07T11:43:17Z

Rf: Created page with "= Introduction = This is a well known open source statistics packages and there is abundant information on the internet about using it. Marvin's R version is 3.2.1 which dat..."

2017-02-07T11:14:17Z

Created page with "= Introduction = This is a well known open source statistics packages and there is abundant information on the internet about using it. Marvin's R version is 3.2.1 which dat..."

New page

= Introduction =

This is a well known open source statistics packages and there is abundant information on the internet about using it.

Marvin's R version is 3.2.1 which dates from mid 2015. Despite this being a little old now (early 2017), it has a very large number of libraries installed, and these are kept up to date.

Nevertheless, the Bioconductor project has been forging ahead recently issues started to appear relating to the age of the the 3.2.1 version.
= Installation notes =

The new 3.2.5 version

← Older revision		Revision as of 15:18, 7 February 2017
Line 44:		Line 44:
	* '''biocLite()''' will install all the base Bioconductor packages if they haven't been installed yet.		* '''biocLite()''' will install all the base Bioconductor packages if they haven't been installed yet.

−	From then on, installing the following modules will in their turn install alot of necessary Bioconductor packages (~~beyoind~~ the base installed by BiocLite().	+	From then on, installing the following modules will in their turn install alot of necessary Bioconductor packages (beyond the base installed by the BiocLite() command.

← Older revision		Revision as of 14:44, 7 February 2017
Line 44:		Line 44:
	* '''biocLite()''' will install all the base Bioconductor packages if they haven't been installed yet.		* '''biocLite()''' will install all the base Bioconductor packages if they haven't been installed yet.

−	From then on, installing	+	From then on, installing the following modules will in their turn install alot of necessary Bioconductor packages (beyoind the base installed by BiocLite().

← Older revision		Revision as of 14:28, 7 February 2017
Line 43:		Line 43:
	* the '''source''' is a special repostiory loading statement		* the '''source''' is a special repostiory loading statement
	* '''biocLite()''' will install all the base Bioconductor packages if they haven't been installed yet.		* '''biocLite()''' will install all the base Bioconductor packages if they haven't been installed yet.
		+
		+	From then on, installing

@@ Line 21: / Line 21: @@
 Note that the OpenBLAS link is a symbolic links from libRblas.so to the libopenblas.so. This must be done
 Rmpi note
   install.packages("Rmpi", configure.args = c("--with-Rmpi-include=/usr/local/Modules/modulefiles/tools/openmpi/2.0.1/include/", "--with-Rmpi-libpath=/usr/local/Modules/modulefiles/tools/openmpi/2.0.1/lib/", "--with-Rmpi-type=OPENMPI"))

← Older revision		Revision as of 12:30, 7 February 2017
Line 23:		Line 23:

	Rmpi note		Rmpi note
−	install.packages("Rmpi", configure.args = c("--with-Rmpi-include=/usr/~~include~~/openmpi~~-x86_64~~/", "--with-Rmpi-libpath=/usr/~~lib64~~/openmpi/lib/", "--with-Rmpi-type=OPENMPI"))	+	install.packages("Rmpi", configure.args = c("--with-Rmpi-include=/usr/local/Modules/modulefiles/tools/openmpi/2.0.1/include/", "--with-Rmpi-libpath=/usr/local/Modules/modulefiles/tools/openmpi/2.0.1/lib/", "--with-Rmpi-type=OPENMPI"))

@@ Line 8: / Line 8: @@
 = Installation notes =
 The new 3.2.5 version
-* compiled with gcc version 4.8.2 (Using Red Hat's Development Toolkit). Make sure it is not version 4.4.7, as this lacks the crucial C++11 additions. (Check for this using<pre>&#10;gcc -v</pre>
+* compiled with gcc version 4.8.2 (Using Red Hat's Development Toolkit). Make sure it is not version 4.4.7, as this lacks the crucial C++11 additions. Check for this using<pre>&#10;gcc -v</pre>
-* linked to OpenBLAS/0.2.19
+Note that the OpenBLAS link is a symbolic links from libRblas.so to the libopenblas.so. This must be done