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mssm

This package provides tools for the identification of submatrix of maximal sum. A submatrix is a rectangular, non-necessarily contiguous, subset of rows and of columns of a (larger) matrix. The submatrices that are searched for are of maximal sum. A submatrix is of maximal sum if the sum of its entries (selected from the original matrix) is of maximal sum. This package is a R wrapper for the Scala implementation originally provided.

Installation

Recommended installation of the latest development version is done via

> library(devtools)
> install_github("vbranders/mssm")

in R. If everything went fine, you can now load the package without any error:

> library(mssm)

If errors are raised, keep reading.

Issues with rJava

The mssm package has the dependency rJava. Although the installation should be fine in most cases, there are many posts dedicated to fixing rJava installation. We have three suggestions regarding possible issues while installing rJava:

  1. As first step, consider the next sections that propose a generic solution to most common issues.
  2. Read the rJava github for installation instructions and documentation.
  3. Search for solutions to your (possibly already solved) specific error.

Common issue

As the package interfaces R and Java, a JDK (or Java Development Kit) should be available to R. This means that you should have a JDK installed and the environment variable JAVA_HOME should point to the JDK location. In most cases, this requirement is not met, which leeds to an error during the installation.

If you hadn't installed a JDK yet, you should download and install the latest version (we consider here the JDK version 1.8.0_181). If you have a JDK installed but you don't know the version, or you don't know if you have a JDK, just type in your favorite command line interface:

$ java -version

To detect the current Java setup and update the corresponding configuration in R, type:

$ R CMD javareconf -e

This might have fixed the rJava installation issue, but you most probably should continue before re-trying to install mssm. Note: if you are using RStudio, consider restarting R session before any re-installation of mssm or rJava.

Fixing on Mac OS X

You know need to set up the JAVA_HOME environment variable so that it contains the path to your JDK. To get the actual path to the JDK (assuming it is version 1.8.0_181) and then the value of the JAVA_HOME variable, type:

$ /usr/libexec/java_home -v 1.8.0
$ echo $JAVA_HOME

Both should match. If not, the JAVA_HOME must be updated as follows:

$ export JAVA_HOME=`/usr/libexec/java_home -v 1.8.0`

Then, continue with the Updating configuration section.

Fixing on Linux (or associated)

Dynamic libraries locations are referenced in the LD_LIBRARY_PATH environment variable. To provide R and rJava an access to the java dynamic library, the environment variable must be updated as follows:

$ export LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH

Once done, continue with the Updating configuration section.

Updating configuration

Now that environment variables are updated, the new Java setup must be detected and the associated R configuration must be updated:

$ R CMD javareconf -e

The problem should be fixed now and you can finally install and use the mssm package as explained in the Installation section. Note: the distinction between Max OS X and Linux is motivated by there different most frequent issues. Both fixes can be considered on both Mac OS X and Linux (but some commands might requires adaptations).

To ensure that rJava (after installation) uses the right JDK version, you can type the following lines in R and check that the output match your expectations:

> library(rJava)
> .jinit(".")
> .jcall("java/lang/System", "S", "getProperty", "java.version")

Bug reports

Please use mssm GitHub issues page to report bugs.