Solved. Thanks a lot! On Wed, Jul 31, 2013 at 8:06 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Olivier, > > > On 7/31/2013 11:54 AM, Olivier [guest] wrote: > >> I'm having problems installing genefilter. Grateful if you could help. >> Thanks. >> >>> biocLite('genefilter') >>> >> ... (ommitted lines for clarity) >> * installing *source* package ‘XML’ ... >> ** package ‘XML’ successfully unpacked and MD5 sums checked >> >> checking for gcc... gcc >> checking for C compiler default output file name... >> rm: cannot remove `a.out.dSYM': Is a directory >> 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 pkg-config... /usr/bin/pkg-config >> checking for xml2-config... no >> Cannot find xml2-config >> > > This is your hint ^^^^^^^^^^^ > > If you google ubuntu xml2-config, you will see that you need to do > > apt-get install libxml2-dev > > Best, > > Jim > > > ERROR: configuration failed for package ‘XML’ >> * removing ‘/home/olivier/R/x86_64-pc-**linux-gnu- library/3.0/XML’ >> ERROR: dependency ‘XML’ is not available for package ‘annotate’ >> * removing ‘/home/olivier/R/x86_64-pc-**linux-gnu-library/3.0/** >> annotate’ >> ERROR: dependency ‘annotate’ is not available for package >> ‘genefilter’ >> * removing ‘/home/olivier/R/x86_64-pc-**linux-gnu-library/3.0/** >> genefilter’ >> >> >> The downloaded source packages are in >> ‘/tmp/Rtmpylk0c1/downloaded_**packages’ >> >> Warning messages: >> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> installation of package ‘XML’ had non-zero exit status >> >> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> installation of package ‘annotate’ had non-zero exit status >> >> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> installation of package ‘genefilter’ had non-zero exit status >> >> >> -- output of sessionInfo(): >> >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> LC_TIME=en_GB.UTF-8 >> [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 >> LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] tools parallel stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] BiocInstaller_1.10.3 ALL_1.4.14 Biobase_2.20.1 >> BiocGenerics_0.6.0 >> [5] limma_3.16.7 >> >> -- >> 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 > > [[alternative HTML version deleted]]