[BioC] Updating Package Versions from SVN

James W. MacDonald jmacdon at uw.edu
Tue Mar 27 01:26:49 CEST 2012

Hi Chris,

On 3/26/2012 7:04 PM, chris_utah wrote:
> Hi,
> I am attempting to update DESeq with the latest version in found in Subversion.  I have downloaded the latest version of DESeq to my hard drive using:
> svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DESeq
> What steps do I take to incorporate the features of the new version into my existing DESeq package?

You don't give your operating system, so it isn't possible to give the 
exact commands you will need. So I will just randomly assume you are on 
Linux, because you wouldn't be cool if you weren't. </ignite flame war> ;-D

You need to install the package now, so you will need to change to the 
directory you put DESeq into, and then type

/path/to/R/bin/R CMD build DESeq

which will build a tarball of the package, called something like 
DESeq_some_ver_here.tar.gz that can then be installed using

/path/to/R/bin/R CMD INSTALL DESeq_some_ver_here.tar.gz

Here I am assuming that R isn't in your path. Perhaps it is, in which 
case you could just use R CMD build, etc.

If you don't really care about building vignettes and such things, you 
can install directly (e.g., R CMD INSTALL DESeq). In addition, if your R 
is installed system-wide and you use a personal library, you will have 
to pass an additional argument showing where your library is located, 
something like

R CMD INSTALL -l /path/to/library DESeq

Or you could install at an R prompt by starting R in the correct 
directory (or using setwd()), and then doing

install.packages("DESeq", repos=NULL)

which will use your personal library automagically.

If you are on either MacOS or Windows, things will be slightly different 
and more complicated. See the MacOS or Windows FAQ on r-project.org, 
specifically the part about building R.



> Thank you very much for any help.
> best wishes,
> Chris
> Christopher Gregg, PhD.
> New York Stem Cell Foundation-Robertson Investigator
> Assistant Professor, Neurobiology and Anatomy
> Adjunct Assistant Professor, Human Genetics
> 323 Wintrobe Bldg 530
> University of Utah, School of Medicine
> 20 North 1900 East, 401 MREB
> Salt Lake City, Utah 84132-3401
> phone: (801) 581-8212
> fax: (801) 585-9736
> ------------------------------------
> Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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