Dear BioC I am having problems installing gplots and gdata on a Linux Ubuntu 9.10 machine. The installation runs as far as installing help indices where it runs out of memory (4Gb) and reports a segmentation error (see below). * Installing *source* package ‘gdata’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices >>> Building/Updating help pages for package 'gdata' Formats: text html latex example Args text html latex example ConvertMedUnits text html latex example MedUnits text html latex example aggregate.table text html latex example bindData text html latex example cbindX text html latex example combine text html latex example drop.levels text html latex example elem text html latex example env text html latex example frameApply text html latex example gdata-package text html latex getDateTimePart text html latex example humanReadable text html latex example installXLSXsupport text html latex example interleave text html latex example Out of memory! Segmentation fault ERROR: building help failed for package ‘gdata’ * Removing ‘/home/ross/R/i486-pc-linux-gnu-library/2.9/gdata’ * Installing *source* package ‘gplots’ ... ** R ** data ** inst ** preparing package for lazy loading Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'gdata' Error : package 'gdata' could not be loaded ERROR: lazy loading failed for package ‘gplots’ * Removing ‘/home/ross/R/i486-pc-linux-gnu-library/2.9/gplots’ The downloaded packages are in ‘/tmp/Rtmp49KOvi/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'gdata' had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'gplots' had non-zero exit status The sessionInfo is as follows: > sessionInfo() R version 2.9.2 (2009-08-24) i486-pc-linux-gnu locale: LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Revobase_0.2-1 loaded via a namespace (and not attached): [1] tools_2.9.2 Many thanks for your help with this. Ross Dr Ross Chapman BSc, MRes, PhD. EcoGeonomix PO BOX 8058 Ferntree Gully Victoria 3156 Australia www.ecogeonomix.com [[alternative HTML version deleted]]

Hi, On Sun, Sep 5, 2010 at 10:13 PM, Ross Chapman <ross.chapman at="" ecogeonomix.com=""> wrote: > Dear BioC > > I am having problems installing gplots and gdata on a Linux Ubuntu 9.10 > machine. > > The installation runs as far as installing help indices where it runs > out of memory (4Gb) and reports a segmentation error (see below). Wow ... that's kind of crazy ... not sure what's cuasing that, but: <snip> >> sessionInfo() > R version 2.9.2 (2009-08-24) > i486-pc-linux-gnu You might want to consider upgrading to the latest R (2.11.1), if you can, since the latest version of R is the one that's typically "most supported" by bioconductor. Not sure if that'll help you here, but it's easy enough to do and probably best in the long run anyway :-) -- 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