Hello group, I am having problems installing the GOstat package , I had similar problems for the GO package earlier but it got solved after I had updated my version of R to 2.9. I wanted to know whether the GOstat command has deprecated ,, if yes what is the new command for the same ????? Basically i wanted to use the GOgraph command which came under the GOstat package... Any advice will be greatly helpful & appreciated Yours hopefully, A.Ashwin Department Of Biotechology MLSC Manipal University Karnataka INDIA [[alternative HTML version deleted]]

Hi Ashwin, On May 17, 2009, at 12:51 AM, Ashwin Kumar wrote: > Hello group, > I am having problems installing the GOstat > package , I > had similar problems for the GO package earlier but it got solved > after I > had updated my version of R to 2.9. > I wanted to know whether the GOstat command has deprecated ,, if yes > what is > the new command for the same ????? Basically i wanted to use the > GOgraph > command which came under the GOstat package... It might be just a typo, but the name of the package you are trying to install is GOstats (note you're missing the s). So, with that said, what problems are you having installing the package? Perhaps giving us more details will help smoke out the problem. The GOstats package is installed on my machine just fine (Intel Mac/R 2.9.0). -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos

Hello group , I am still having problems with installing the GOstats package & its not a typo error ... I am pasting my workspace image along with the error it shows: > source("http://bioconductor.org/biocLite.R") Warning messages: 1: In safeSource() : Redefining ‘biocinstall’ 2: In safeSource() : Redefining ‘biocinstallPkgGroups’ 3: In safeSource() : Redefining ‘biocinstallRepos’ > biocLite("GOstats") Running biocinstall version 2.4.10 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/home/mlscub1/R/i486-pc-linux-gnu-library/2.9' also installing the dependencies ‘XML’, ‘GSEABase’, ‘Category’ trying URL ' http://bioconductor.org/packages/2.4/extra/src/contrib/XML_2.3-0.tar.g z' Content type 'application/x-gzip' length 659797 bytes (644 Kb) opened URL ================================================== downloaded 644 Kb trying URL ' http://bioconductor.org/packages/2.4/bioc/src/contrib/GSEABase_1.6.0.t ar.gz' Content type 'application/x-gzip' length 174211 bytes (170 Kb) opened URL ================================================== downloaded 170 Kb trying URL ' http://bioconductor.org/packages/2.4/bioc/src/contrib/Category_2.10.0. tar.gz ' Content type 'application/x-gzip' length 458431 bytes (447 Kb) opened URL ================================================== downloaded 447 Kb trying URL ' http://bioconductor.org/packages/2.4/bioc/src/contrib/GOstats_2.10.0.t ar.gz' Content type 'application/x-gzip' length 2404620 bytes (2.3 Mb) opened URL ================================================== downloaded 2.3 Mb * Installing *source* package ‘XML’ ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * Removing ‘/home/mlscub1/R/i486-pc-linux-gnu-library/2.9/XML’ * Installing *source* package ‘GSEABase’ ... ** R ** inst ** preparing package for lazy loading Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : there is no package called 'XML' ERROR: lazy loading failed for package ‘GSEABase’ * Removing ‘/home/mlscub1/R/i486-pc-linux-gnu-library/2.9/GSEABase’ * Installing *source* package ‘Category’ ... ** R ** inst ** preparing package for lazy loading Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Error in loadNamespace(imp[[1L]], c(lib.loc, .libPaths())) : there is no package called 'GSEABase' ERROR: lazy loading failed for package ‘Category’ * Removing ‘/home/mlscub1/R/i486-pc-linux-gnu-library/2.9/Category’ * Installing *source* package ‘GOstats’ ... ** R ** data ** inst ** preparing package for lazy loading Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Error : package 'Category' required by 'GOstats' could not be found ERROR: lazy loading failed for package ‘GOstats’ * Removing ‘/home/mlscub1/R/i486-pc-linux-gnu-library/2.9/GOstats’ The downloaded packages are in ‘/tmp/RtmpykjLAI/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'XML' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'GSEABase' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'Category' had non-zero exit status > library(GOstats) Error in library(GOstats) : there is no package called 'GOstats' Any advice will be greatly appreciated .... Thankfully A.Ashwin MLSC Department of Biotechnology Manipal University INDIA [[alternative HTML version deleted]]