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? 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]]

Hi Chris, On Mon, Mar 26, 2012 at 4:04 PM, chris_utah <chris.gregg at="" neuro.utah.edu=""> 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? Instead of this, it's probably a better idea to open R and type: source("http://bioconductor.org/biocLite.R") biocLite("DESeq") This will give you the latest version of DESeq for the version of R you are running. If you are running a pre-release version of R 2.15, you will get the version of DESeq that is equivalent (within a day) to the one in svn trunk. Dan > > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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> ;-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. Best, Jim > > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099