I tried to install Rgraphviz using your instructions: https://stat.ethz.ch/pipermail/bioconductor/2004-October/006227.html but I keep receiving this error message: * Installing *source* package 'Rgraphviz' ... checking for graphviz... checking for dotneato-config... /usr/bin /dotneato-config /usr/bin/dotneato-config failed configure: error: please specify a valid path to 'dotneato-config' version >= 1.12 using --with-graphviz=DIR ERROR: configuration failed for package 'Rgraphviz' Before I installed graphviz (from sources) -everything OK, I checked $ whereis graphviz (it's OK in /usr/lib/graphviz) and I checked also the content of 'dotneato-config' in /usr/bin for the line of graphviz path and seems to be correct. Any suggestions please ? Liviu

On Dec 14, 2004, at 11:43 AM, Liviu M Vladutu wrote: > > > I tried to install Rgraphviz using your instructions: > https://stat.ethz.ch/pipermail/bioconductor/2004-October/006227.html > > but I keep receiving this error message: > * Installing *source* package 'Rgraphviz' ... > checking for graphviz... checking for dotneato-config... > /usr/bin/dotneato-config > /usr/bin/dotneato-config > failed > Hi, Can you check to be sure that dotneato-config is in your path, Something like: tui:$dotneato-config --cflags -I/usr/local/include/graphviz tui:$dotneato-config --libs -L/usr/local/lib/graphviz -ldotneato Check to make sure that these values are correct (the first should be the location of the include files and the second the location of the libraries). If not, then you need to fix that. If that is ok can you please report the version of graphviz you are using. Robert > configure: error: please specify a valid path to 'dotneato-config' > version >= > 1.12 using --with-graphviz=DIR > ERROR: configuration failed for package 'Rgraphviz' > > > Before I installed graphviz (from sources) -everything OK, I checked > $ whereis graphviz (it's OK in /usr/lib/graphviz) > and I checked also the content of 'dotneato-config' in /usr/bin for > the line of > graphviz path and seems to be correct. > Any suggestions please ? > Liviu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----+

Hi Liviu, I think I had same problem in past and I solved like this: install graphviz package from : http://www.research.att.com/sw/tools/graphviz/download.html go to your linux/unix shell and type : whereis graphviz: it will show something like this: /user/lib/graphviz whatever paht you get...just type export LD_LIBRARY_PATH=/usr/lib/graphviz and from that same shell...try to install Rgraphviz..with: ./configure --prefix=/usr --exec-prefix=/usr make make check all su (change user to super user if you have or just type make install) make install If you still have any problems , let me know..! Saurin Quoting Liviu M Vladutu <vladutu@musc.edu>: > > > I tried to install Rgraphviz using your instructions: > https://stat.ethz.ch/pipermail/bioconductor/2004-October/006227.html > > but I keep receiving this error message: > * Installing *source* package 'Rgraphviz' ... > checking for graphviz... checking for dotneato-config... > /usr/bin/dotneato-config > /usr/bin/dotneato-config > failed > configure: error: please specify a valid path to 'dotneato-config' version > >= > 1.12 using --with-graphviz=DIR > ERROR: configuration failed for package 'Rgraphviz' > > > Before I installed graphviz (from sources) -everything OK, I checked > $ whereis graphviz (it's OK in /usr/lib/graphviz) > and I checked also the content of 'dotneato-config' in /usr/bin for the line > of > graphviz path and seems to be correct. > Any suggestions please ? > Liviu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- |------------------------------------------------ | Saurin Jani | Bioinformatician | | Department of Cell Biology and Anatomy | Medical University of South Carolina (MUSC) | 173 Ashley Ave | Charleston,SC - 29407 (US) | | Email: jani@musc.edu | Phone: (843)792-5483 |------------------------------------------------

Hi, I know that I can extract intensity values using the expression PM <- pm(affybatch.example)[Index,]; Is there any trick to reassigning new intensity values to the CEL file? Thanks for your help, Lana Lana Schaffer Research Specialist The Scripps Research Institute DNA Array Core Facility