Thanks for helping! Updating to 8.04 which comes with R.2.6.2 did the trick. --- Den tirs 1/7/08 skrev Vincent Carey 525-2265 <stvjc at="" channing.harvard.edu="">: > Fra: Vincent Carey 525-2265 <stvjc at="" channing.harvard.edu=""> > Emne: Re: [BioC] cant install Rgraphviz > Til: "Anders Stegmann" <aogr_dk_2000 at="" yahoo.dk=""> > Cc: bioconductor at stat.math.ethz.ch > Dato: tirsdag 1. juli 2008 15.03 > > Can't install ?Rgraphviz_1.18.1? on Ubuntu > 7.10, with R version 2.5.1 (2007-06-27), BioC 2.2 and > graphviz-2.20.2 > > This version of R is now over a year old. Would you please > update? > > Provided you have a clean installation of graphviz and > graphviz-dev > you should be able to get Rgraphviz installed with > biocLite.R > as you attempted. If problems persist with an updated R, > let me know; I have a similar ubuntu and could try to > reproduce. > But I will not back down to R 2.5.1 for this purpose. > > > > > > >When typing this in R: > > > > > > > >source("http://bioconductor.org/biocLite.R") > > > >biocLite("Rgraphviz") > > > > > > > >I get the following output: > > > > > > > >Running biocinstall version 2.0.8 with R version 2.5.1 > > > >Your version of R requires version 2.0 of Bioconductor. > > > >Warning in install.packages(pkgs = pkgs, repos = repos, > dependencies = dependencies, : > > > > argument 'lib' is missing: using > '/usr/local/lib/R/site-library' > > > >trying URL > 'http://bioconductor.org/packages/2.0/bioc/src/contrib/Rgraphviz_1.1 4.1.tar.gz' > > > >Content type 'application/x-gzip' length > 1521762 bytes > > > >opened URL > > > >================================================== > > > >downloaded 1486Kb > > > > > > > >* Installing *source* package 'Rgraphviz' ... > > > >configure: No --with-graphviz option was specified. > Trying to find graphviz using other methods. > > > >checking for pkg-config... /usr/bin/pkg-config > > > >configure: Found graphviz 2.20.2 > > > >configure: We have inferred the following flags for > graphviz > > > >configure: ..PKG_CPPFLAGS=-I/usr/local/include/graphviz > > > >configure: ..PKG_LIBS=-L/usr/local/lib -lgvc -lgraph > -lcdt > > > >configure: creating ./config.status > > > >config.status: creating src/Makevars > > > >** libs > > > >gcc-4.2 -std=gnu99 -I/usr/share/R/include > -I/usr/share/R/include -I/usr/local/include/graphviz > -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -fpic -g -O2 -c > agopen.c -o agopen.o > > > >I filen inkluderet af agopen.c:1: > > > >common.h:41:20: error: gvcint.h: No such file or > directory > > > >common.h:42:21: error: globals.h: No such file or > directory > > > >make: *** [agopen.o] Fejl 1 > > > >chmod: kan ikke tilg? > '/usr/local/lib/R/site-library/Rgraphviz/libs/*': > No such file or directory > > > >ERROR: compilation failed for package > 'Rgraphviz' > > > >** Removing > '/usr/local/lib/R/site-library/Rgraphviz' > > > >** Restoring previous > '/usr/local/lib/R/site-library/Rgraphviz' > > > > > > > >The downloaded packages are in > > > > /tmp/RtmptAYLaf/downloaded_packages > > > >Warning message: > > > >installation of package 'Rgraphviz' had > non-zero exit status in: install.packages(pkgs = pkgs, > repos = repos, dependencies = dependencies, > > > > > > > >I have the files ?gvcint.h? and ?globals.h? as > I've installed ?graphviz-dev? as well. > > > > > >When installing ?Rgraphviz_1.18.1.tar.gz? manually > and trying to configure ?Rgraphviz? with > ?./configure?, I get following output: > > > >configure: No --with-graphviz option was specified. > Trying to find graphviz using other methods. > > > >checking for pkg-config... /usr/bin/pkg-config > > > >configure: Found graphviz 2.20.2 > > > >configure: We have inferred the following flags for > graphviz > > > >configure: ..PKG_CPPFLAGS=-I/usr/local/include/graphviz > > > >configure: ..PKG_LIBS=-L/usr/local/lib -lgvc -lgraph > -lcdt > > > >checking for whether compiler has bool... 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 ANSI C... none needed > > > >checking how to run the C preprocessor... gcc -E > > > >checking for egrep... 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 > > > >yes > > > >configure: creating ./config.status > > > >config.status: creating src/Makevars > > > > > > > >After this I type ?make? and gets output: > > > >make: *** Ingen angivne m?l og ingen makefil fundet. > Stop. > > > >It didn't find a makefile. > > > >What now? > > > > > > > > > > Find din nye laptop p? kelkoo.dk. Se de gode > tilbud her - http://dk.yahoo.com/r/pat/mm > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductorThe > information transmitted in this electronic communication is > intended only > for the person or entity to whom it is addressed and may > contain confidential > and/or privileged material. Any review, retransmission, > dissemination or other > use of or taking of any action in reliance upon this > information by persons or > entities other than the intended recipient is prohibited. > If you received this > information in error, please contact the Compliance > HelpLine at 800-856-1983 and > properly dispose of this information. Tr?nger du til at se det store billede? Kelkoo giver dig gode tilbud p? LCD TV! Se her http://dk.yahoo.com/r/pat/lcd