[BioC] cant install Rgraphviz

[Vincent Carey 525-2265]

> 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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