[BioC] cant install Rgraphviz

Tue Jul 1 15:35:06 CEST 2008

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_1.14.1.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 tilgå
> '/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 mål og ingen makefil fundet.
> Stop.
> >
> >It didn't find a makefile.
> >
> >What now?
> >
> >
> >
> >
> >      Find din nye laptop på kelkoo.dk. Se de gode
> tilbud her - http://dk.yahoo.com/r/pat/mm
> >
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