Hi, I've tried to install the yg98_1.6.8.tar.gz in my linux, but I found the package is missing symbol, refseq and unigene information. When I try to load the symbol for probe ID with annoation package, it reports: Object "yg98SYMBOL" not found. Is this the package problem? So I tried to use the annobuilder. But when I tried to install XML (XML_0.97-0.tar.gz), I have the following errors: > install.packages("XML","~/R") trying URL `http://cran.r-project.org/src/contrib/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 46868 bytes opened URL ================================================== downloaded 45Kb trying URL `http://cran.r-project.org/src/contrib/XML_0.97-0.tar.gz' Content type `application/x-tar' length 556400 bytes opened URL ================================================== downloaded 543Kb * 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 xml2-config... no Cannot find xml2-config ERROR: configuration failed for package 'XML' Has any one have the same problems? Thanks you. Lin

Yes, others have had that problem and searching the mailing list archive would have pointed you to the correct solution. You do not have libxml installed on your computer and you will need to have it installed, the XML package uses software available through libxml. Robert ps did you look at what you did get in the yg98 package and make sure that the information you want is not there (perhaps stored in a different place than you looked?) Reading the manual pages and searching the available mailing list archives is sometimes not an entirely irrelevant exercise. On Jan 27, 2005, at 12:16 PM, Lin Tang wrote: > Hi, > I've tried to install the > 1.6.8.tar.gz in my linux, but I found the > package is missing symbol, refseq and unigene information. When I try > to > load the symbol for probe ID with annoation package, it reports: > > Object "yg98SYMBOL" not found. > > Is this the package problem? > > So I tried to use the annobuilder. But when I tried to install XML > (XML_0.97-0.tar.gz), I have the following errors: > >> install.packages("XML","~/R") > trying URL `http://cran.r-project.org/src/contrib/PACKAGES' > Content type `text/plain; charset=iso-8859-1' length 46868 bytes > opened URL > ================================================== > downloaded 45Kb > > trying URL `http://cran.r-project.org/src/contrib/XML_0.97-0.tar.gz' > Content type `application/x-tar' length 556400 bytes > opened URL > ================================================== > downloaded 543Kb > > * 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 xml2-config... no > Cannot find xml2-config > ERROR: configuration failed for package 'XML' > > > Has any one have the same problems? > > Thanks you. > > Lin > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+