Thanks for sharing your expertise Jim - that solution worked perfectly! On Wed, Aug 14, 2013 at 12:02 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Mark, > > > On 8/14/2013 11:57 AM, Mark Christie [guest] wrote: > >> Hi all, >> >> I have entered dependency hell when trying to install DESEq2. I am using >> Rstudio that is running on linux Mint, with R version 3.0.1. >> >> When I run biocLite(c("DESeq2"), dependencies = TRUE), I get the >> following warnings at the end of what almost seems like a successful >> install (See below). I don't think this problem is specific to DESeq2, but >> does anybody have an idea as to what is going on here. >> >> Warning messages: >> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘RCurl’ had non-zero exit status >> >> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘XML’ had non-zero exit status >> >> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘biomaRt’ had non-zero exit status >> >> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘annotate’ had non-zero exit status >> >> 5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘geneplotter’ had non-zero exit status >> >> 6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘DEXSeq’ had non-zero exit status >> >> 7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘genefilter’ had non-zero exit status >> >> 8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘DESeq’ had non-zero exit status >> >> 9: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘DESeq2’ had non-zero exit status >> >> 10: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... : >> installation of package ‘pasilla’ had non-zero exit status >> >> 11: installed directory not writable, cannot update packages 'MASS', >> 'spatial' >> > > You don't show the part of the install output that is of interest, but it > is likely that you don't have the xml headers installed. A quick look > indicates that Mint is a Debian offshoot, so something like > > sudo apt-get install libxml2-dev > > should do the trick. > > Best, > > Jim > > > >> Many Thanks! >> >> Mark Christie >> >> -- output of sessionInfo(): >> >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.10.3 >> >> loaded via a namespace (and not attached): >> [1] tools_3.0.1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<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 > > -- Mark R. Christie, PhD Department of Zoology, Oregon State University http://www.science.oregonstate.edu/~christim/ [[alternative HTML version deleted]]