I am trying to install the XML and AnnBuilder packages in a SUN SOLARIS. I have problems installing the XML. I got these error messages (please see below). I can guess that the problem is due to this: checking for xml-config... no checking for xml2-config... no Cannot find xml2-config I would appreciate any hint on how to fix this problem. Thanks a lot. Roger ############################################# > options(CRAN = "http://cran.r-project.org/") > install.packages("XML", "~/r181/library") trying URL `http://cran.r-project.org//src/contrib/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 156484 bytes opened URL .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .. downloaded 152Kb trying URL `http://cran.r-project.org//src/contrib/XML_0.95-6.tar.gz' Content type `application/x-tar' length 551360 bytes opened URL .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... ........ downloaded 538Kb * Installing *source* package 'XML' ... checking for gcc... gcc checking for C compiler default output... 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 ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for xml-config... no checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package 'XML' ** Removing '/.../dce.psu.edu/fs/users/r/l/rlv10/r181/~/r181/library/XML' ################################3 Roger L. Vallejo, Ph.D. Assist. Professor of Genomics & Bioinformatics The Pennsylvania State University Department of Dairy & Animal Science 305 Henning Building University Park, PA 16802 Phone: (814) 865-1846 Fax: (814) 863-6042 Email: rvallejo@psu.edu <mailto:rvallejo@psu.edu> [[alternative HTML version deleted]]

You need to install the GNOME XML libraries or a similar library (I thought expat might work, but maybe not). best, -tony "Roger Vallejo" <rvallejo@psu.edu> writes: > I am trying to install the XML and AnnBuilder packages in a SUN SOLARIS. > I have problems installing the XML. I got these error messages (please > see below). > > I can guess that the problem is due to this: > > > > checking for xml-config... no > > checking for xml2-config... no > > Cannot find xml2-config > > > > I would appreciate any hint on how to fix this problem. Thanks a lot. > > Roger > > > > ############################################# > >> options(CRAN = "http://cran.r-project.org/") > >> install.packages("XML", "~/r181/library") > > trying URL `http://cran.r-project.org//src/contrib/PACKAGES' > > Content type `text/plain; charset=iso-8859-1' length 156484 bytes > > opened URL > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .. > > downloaded 152Kb > > > > trying URL `http://cran.r-project.org//src/contrib/XML_0.95-6.tar.gz' > > Content type `application/x-tar' length 551360 bytes > > opened URL > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... .......... .......... > > .......... .......... .......... ........ > > downloaded 538Kb > > > > * Installing *source* package 'XML' ... > > checking for gcc... gcc > > checking for C compiler default output... 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 ANSI C... none needed > > checking how to run the C preprocessor... gcc -E > > checking for xml-config... no > > checking for xml2-config... no > > Cannot find xml2-config > > ERROR: configuration failed for package 'XML' > > ** Removing > '/.../dce.psu.edu/fs/users/r/l/rlv10/r181/~/r181/library/XML' > > ################################3 > > > > Roger L. Vallejo, Ph.D. > > Assist. Professor of Genomics & Bioinformatics > > The Pennsylvania State University > > Department of Dairy & Animal Science > > 305 Henning Building > > University Park, PA 16802 > > Phone: (814) 865-1846 > > Fax: (814) 863-6042 > > Email: rvallejo@psu.edu <mailto:rvallejo@psu.edu> > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}

On Wed, Feb 04, 2004 at 01:59:49PM -0500, Roger Vallejo wrote: > I am trying to install the XML and AnnBuilder packages in a SUN SOLARIS. > I have problems installing the XML. I got these error messages (please > see below). > > I can guess that the problem is due to this: > > > > checking for xml-config... no > > checking for xml2-config... no > > Cannot find xml2-config > > I would appreciate any hint on how to fix this problem. Thanks a lot. > Installing R packages on Solaris (indeed any *NIX system) may require the compilation of some source code. This may require additonal libraries avaliable. In this case you need the prescence of either libxml or libxml2. I'm not too familiar with Solaris, but I am pretty sure one of these packages may be download from Sun's site (or some other repository). Follow the installation instructions, and it should work. In case you still have problems (and have installed the packages), the problem may be that the compiler is unable to find said libraries. This may be solved by configuring your system - one possibility is setting the environment LD_LIBRARY_PATH to a suitable value. -- Kasper Daniel Hansen, Research Assistent Department of Biostatistics, University of Copenhagen