R software by Henrik Bengtsson

Henrik Bengtsson, 2012-05-04

Active packages

Please know that the packages that I am actively developing are available on CRAN and Bioconductor, e.g. R.methodsS3, R.oo, R.utils, R.cache, R.devices, R.rsp, R.matlab, matrixStats, aroma.light, aroma.affymetrix, aroma.cn, aroma.core, and PSCBS. I am a co-developer of other packages, e.g. affxparser, ACNE and calmate.

I also maintain the Aroma Project which provides a suite of packages (of which the majority of them are available from CRAN and Bioconductor).


Almost all your needs should be addressed above. If not, keep reading.

Legacy packages

In the past I've developed several other R packages that are no longer developed. See below table. For backward compatibility, I will try my best to keep these legacy packages working with newer version of R, but please do not develop new packages that rely on these. If you find something valuable in one of the below legacy packages that you think should be on CRAN/Bioconductor, drop me a note and convince me.

Name Description Notes Status
aroma An R Object-oriented Microarray Analysis package for two-color arrays. NOTE: This predated the Aroma Project and is independent of it.
100% R alpha, beta & stable
aroma.Base A generic R plugin dispatcher for BASE (v1).
100% R beta
R.audio Audio and sound classes. 100% R
trial: alpha & beta
R.basic Stand-alone basic functions. NOTE: Many of these functions have now been moved to R.utils and aroma.light. 100% R, contains deprecated methods beta & stable
R.batch Methods to run batch jobs in R. The package provides methods to batch run R scripts in a straightforward manner. A job batch is defined by a root directory containing subdirectories todo/, running/, finished/, failed/, src/ among others. A job to be processed is a directory placed in todo/. A job is processed by moving it to running/, then sourcing the R files in src/ (containing common code) and then the ones in the job directory (contain job specific code), in which a function onRun() has to be defined, which is then called. Succesfully jobs end up in finished/ whereas failed jobs in failed/. 100% R beta
R.colors Color and color filter classes. 100% R trial: alpha & beta
R.graphics Graphics classes. NOTE: Many of these functions have now been moved to R.utils and R.devices. 100% R, contains deprecated methods alpha & beta
R.image Classes and methods for bitmap images. 100% R trial: alpha & beta
R.io File, connection and I/O classes. NOTE: Many of the methods have been moved to R.utils and R.rsp. 100% R, contains deprecated methods alpha & beta

Requirements, Dependencies and Package versions

All of the above packages required that you have a very recent version of R installed. If you have problem with some my packages and you run a more than 10 months old version of R, please do not expect me to troubleshoot it for you. To find out what the latest version is for a given package or to see what packages a certain package depends on, please see the PACKAGES file.

Installation and updates

To install the latest (=devel) version of all the above package, do
To install some of the packages including all packages they depend on, do
hbLite(c("R.oo", "R.utils"))

Aditional options: To install the CRAN versions, if they exists, add argument CRAN=TRUE. To force a re-installation of some of the packages, add arguments force=TRUE.

If the above does not work for you, please see Frequently Asked Questions below.

Source Code

To get hold off the source code of the latest version of a package (or a bundle), do



Contributions are appreciated. Please make sure you are working with the latest version. Minor contributions will be acknowledged and major will make you a co-author.

Frequently Asked Questions

FAQ #1. hbLite() fails to install your packages

Make sure you call the above source() command too. If for some reason it still wont work, see FAQ #2 below. If that won't work, please check you firewall and make sure your proxy settings are correct. If you are on Windows, please see Section "2.19 The Internet download functions fail" in "R for Windows FAQ", which you get by calling help.start().

FAQ #2. Can I install your package using install.packages()?

Sure. The repository is at http://www.braju.com/R/repos/, e.g.

install.packages(c("R.oo", "R.utils"), contriburl="http://www.braju.com/R/repos/")

Make sure to all install required package first (hbLite() takes care of this for you).

FAQ #3. Can I install your package using Rgui?

No, except for the few of them that are on CRAN.

FAQ #4. How do I update all of your packages?

To update all installed packages (from here) and their required packages, do:


The classic way to do this is to call update.packages(contriburl="http://www.braju.com/R/repos/").

FAQ #5. Where is your bundle R.classes?

The R.classes bundle is deprecated since 2005-07-21 (v0.62) in favor of standalone packages. The bundle was created so that the aroma package could be installed in a simple way. It contains packages R.oo, R.audio, R.basic, R.batch, R.colors, R.graphics, R.image, R.io, R.lang, R.matlab, R.ui as they were at the time. However, now since some of these packages are now used not only by aroma users, I have decided to discontinue the bundle.

If you still insist to install the bundle, do

install.packages("R.classes", contriburl="http://www.braju.com/R/repos/R.classes")

FAQ #6. How do I get hold of previous versions of a package?

To get hold off the source code or a binary installation of an older version of a package (or a bundle), do

hbGet("aroma.Base", "0.4.1", "tar.gz")   # Source
hbGet("aroma.Base", "0.4.1", "zip")      # Windows binary

If the above for some reason does not work, you can download the files manually by for example http://www.braju.com/R/repos/aroma.Base_0.4.1.tar.gz.

The web server does unfortunately not allow us to list existing packages, so for now you have to set the version number by trial and error to see if it exists.

Contact information

To contact me regarding one of the package, please email me at henrikb @ braju . com.

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