nandb

An R package for performing number and brightness analysis as in Digman et al. 2008.

Installation

Platform Dependencies

Mac OS X

Mac OS X comes with a legacy Apple Java 6. Update your Java installation to a newer version provided by Oracle.

1. Install Oracle JDK.

2. Update R Java configuration by executing from the command line (you might have to run it as a super user by prepending sudo depending on your installation).

   R CMD javareconf

3. Re-install rJava from sources in order to properly link to the non-system Java installation.

   install.packages("rJava", type="source")

4. Then, to make everything work with Rstudio, run

   sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib

   (taken from http://stackoverflow.com/questions/30738974/rjava-load-error-in-rstudio-r-after-upgrading-to-osx-yosemite).

You can verify your configuration by running the following commands. This should return the Java version string corresponding to the one downloaded and installed in step 1.

library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
## [1] "1.8.0_112-b16" 

Thanks to @aoles for these instructions. Check out his great work on image analysis in R at https://github.com/aoles.

Linux

1. Install the latest JDK. Be sure to install both 32-bit and 64-bit.

2. On Ubuntu (similarly for other debian linux), you need to do:

   sudo apt-get update
   sudo apt-get install libssl-dev libtiff5-dev libfftw3-dev 
   sudo apt-get install libcurl4-openssl-dev libxml2-dev 
   sudo apt-get install default-jre default-jdk libboost-all-dev

Windows

1. Install the latest JDK. Be sure to install both 32-bit and 64-bit.

2. Go to https://cran.r-project.org/bin/windows/Rtools/ and install the latest version of Rtools.

All Platforms

Then, everyone, open R and run:

source("https://bioconductor.org/biocLite.R")
biocLite(c("EBImage", "BiocParallel"))
install.packages("nandb")

If you get a message saying Update all/some/none? [a/s/n]:, type a. If you get the chance to install some packages from source, it's safest to decline.

Problems

If you run into problems during your installation, it's most likely that your installation of rJava didn't work. Try running install.packages("rJava") and try to work through the errors there. If that still doesn't work, try googling "install rJava" for your operating system e.g. "install rJava Ubuntu". The second most likely culprit is EBImage so similarly have a google of "install EBImage". If you get these to work, then try the installation instructions again. If you still can't get it to work, feel free to contact me via the issues page associated with this repo.

Updates

To update the package, you just need to do the same thing:

source("https://bioconductor.org/biocLite.R")
biocLite(c("EBImage", "BiocParallel"))
install.packages("nandb")

Use

For the lowdown on how to use this package, you should read the package vignettes. Once you've installed the package, you can browse them using vignette(package = "nandb").