dear List, I am trying to install the package girafe from bioconductor but I have been unsuccessful. I first tried via biocLite but I am getting the error : package not available (see pasted message bellow) and then I have tried to install from source. I have downloaded the tar.gz file and biocLite("girafe") I am getting another error: Creating a new generic function for "plot" in "girafe" Warning in omitted & is.na(match(signature[omitted], c("ANY", "missing"))) : longer object length is not a multiple of shorter object length Error in conformMethod(signature, mnames, fnames, f, fdef, definition) : In method for function "coverage": formal arguments omitted in the method definition cannot be in the signature (start = "NA", end = "NA") Error : unable to load R code in package 'girafe' ERROR: lazy loading failed for package ‘girafe’ * removing ‘/usr/local/lib/R/site-library/girafe’ Warning message: In install.packages("girafe_1.0.0.tar.gz") : installation of package 'girafe_1.0.0.tar.gz' had non-zero exit status thanks in advance for your help. Information about session info is in the end of this message With kind regards, Andreia error message from biocLite("girafe"): ---------------------------------------------------------------------- ------- Using R version 2.10.1, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "girafe" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '/usr/local/lib/R/site-library' Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘girafe’ is not available sessionInfo: sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.1 -- -------------------------------------------- Andreia J. Amaral Unidade de Imunologia Clínica Instituto de Medicina Molecular Universidade de Lisboa email: andreiaamaral@fm.ul.pt andreia.fonseca@gmail.com [[alternative HTML version deleted]]

Hi Andreia, On Thu, Jun 17, 2010 at 10:56 AM, Andreia Fonseca <andreia.fonseca at="" gmail.com=""> wrote: > dear List, > > I am trying to install the package girafe from bioconductor but I have been > unsuccessful. <snip> > error message from biocLite("girafe"): > -------------------------------------------------------------------- --------- > Using R version 2.10.1, biocinstall version 2.5.10. > Installing Bioconductor version 2.5 packages: > [1] "girafe" > Please wait... I've just successfully installed girafe on my system: * OS X.6.3 * R 2.11.1 I'd try upgrading your version of R to the latest (2.11.1) and reinstall biocondcutor + giraffe before burning too much time trying to smoke out any other things. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact