Thanks Dan. It works now. Holly On 04/06/2012 07:09 PM, Dan Tenenbaum wrote: > Hi Holly, > > > On Fri, Apr 6, 2012 at 1:20 PM, Holly<xyang2 at="" uchicago.edu=""> wrote: >> Hi, >> >> I recently reinstall my machine and cannot figure out how to make Rgraphviz >> work. Following is the information, Please help! >> >> Thanks. >> >> >> $ sudo apt-get install graphviz >> # it installed the by default the 2.26.3-5ubuntu4 >> $ whereis graphviz >> graphviz: /usr/lib/graphviz /usr/share/graphviz >> /usr/share/man/man7/graphviz.7.gz >> >> >> $R >>> source("http://bioconductor.org/biocLite.R") >> BiocInstaller version 1.4.3, ?biocLite for help >>> biocLite("Rgraphviz") >> BioC_mirror: http://bioconductor.org >> Using R version 2.15, BiocInstaller version 1.4.3. >> Installing package(s) 'Rgraphviz' >> trying URL >> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rgraphv iz_1.34.0.tar.gz' >> Content type 'application/x-gzip' length 694533 bytes (678 Kb) >> opened URL >> ================================================== >> downloaded 678 Kb >> >> * installing *source* package ?Rgraphviz? ... >> checking for gcc... gcc >> checking for C compiler default output file name... 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 grep that handles long lines and -e... /bin/grep >> checking for egrep... /bin/grep -E >> checking for ANSI C header files... yes >> checking for sys/types.h... yes >> checking for sys/stat.h... yes >> checking for stdlib.h... yes >> checking for string.h... yes >> checking for memory.h... yes >> checking for strings.h... yes >> checking for inttypes.h... yes >> checking for stdint.h... yes >> checking for unistd.h... yes >> checking for stdbool.h that conforms to C99... yes >> checking for _Bool... yes >> checking for whether compiler has bool... yes >> configure: No --with-graphviz option was specified. Trying to find Graphviz >> using other methods. >> checking for pkg-config... /usr/bin/pkg-config >> Package libgvc was not found in the pkg-config search path. >> Perhaps you should add the directory containing `libgvc.pc' >> to the PKG_CONFIG_PATH environment variable >> No package 'libgvc' found >> configure: pkg-config was not able to find the Graphviz library libgvc. This >> either indicates that Graphviz is old or that something is wrong. Verify >> Graphviz is installed and that PKG_CONFIG_PATH is correct. >> checking for dotneato-config... no >> configure: dotneato-config not found in PATH. >> configure: Using default directory /usr/local, consider specifiying >> --with-graphviz >> configure: error: /usr/local/bin/dot not found. Check Graphviz installation. >> ERROR: configuration failed for package ?Rgraphviz? >> * removing ?/usr/local/lib/R/site-library/Rgraphviz? >> >> The downloaded source packages are in >> ?/tmp/Rtmp8PFzCV/downloaded_packages? >> Warning message: >> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> installation of package ?Rgraphviz? had non-zero exit status >> >>> sessionInfo() >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] 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_1.4.3 >> >> loaded via a namespace (and not attached): >> [1] tools_2.15.0 >> > I think you need the graphviz-dev package as well: > > sudo apt-get install graphviz-dev > > Dan > > >> ========================================= >> Xinan "Holly" Yang, Ph.D. >> Research Associate (Assistant Professor) >> The University of Chicago Departments of Pediatrics >> Section of Hematology/Oncology >> 900 East 57th Street, KCBD Room 5121 >> Chicago, Illinois 60637 >> Phone: 773/702-5960 >> FAX: 773/834-1329 >> xyang2 at uchicago.edu >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor