[BioC] Rgraphviz on Fedora Core 6

[Byron Wallace]

Thank you so much! You were exactly right about bioconductor 1.8, and
I resolved the issue by installing graphviz 2.8. However, I've
unfortunately encountered another issue. After I succesfully install
both 'graph_1.10.6' and 'Rgraphviz_1.10.0', I start R (v 2.4) and
attempt to run the install script to install all the needed
bioconductor packages. Here I get an error telling me that the graph
library is not installed (see below). I'm lost because I the R CMD
INSTALL for the graph library completes successfully. Any insight
here? Thank you again for your time.

> source("install.R")
> install()
checking for installed packages...
checking for graph: ...Error in install() :
ERROR: library graph not installed! install graph package before
running this script!
In addition: Warning message:
there is no package called 'graph' in: library(package, lib.loc =
lib.loc, character.only = TRUE, logical = TRUE,



On 1/29/07, Li.Long at isb-sib.ch <Li.Long at isb-sib.ch> wrote:
>
> Hi,
>
> My guess is that you are trying to install a very old Rgraphviz package
> (bioconductor 1.8?) with the latest graphviz release...  I don't think it
> has anything to do with Fedora 6 core.
>
> You could try to install Rgraphviz-1.12.3 which has been updated to work
> with latest graphviz release.  Or try to find a download for an old
> graphviz, probably 2.8 or so.
>
> Li
>
>
>
> > Hi all -- I'm having problems installing Rgraphviz on Fedora 6 core.
> > Below is the command line interaction, if anyone has any insight I
> > would greatly appreciate it. Thank you.
> >
> > [CARMA at d-p-13-16 R-Install]$ su root R CMD INSTALL Rgraphviz_1.10.0.tar.gz
> > * Installing *source* package 'Rgraphviz' ...
> > checking for graphviz... checking for dotneato-config... not found
> > checking for pkg-config... /usr/bin/pkg-config
> > configure: creating ./config.status
> > config.status: creating src/Makevars
> > ** libs
> > gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/include/graphviz
> >  -DGRAPHVIZGT_2_4 -I/usr/local/include    -fpic  -O3 -g -std=gnu99 -c
> > Rgraphviz.c -o Rgraphviz.o
> > In file included from common.h:29,
> >                  from Rgraphviz.c:1:
> > /usr/include/graphviz/gvcint.h:30: error: expected
> > specifier-qualifier-list before 'gvlayout_engine_t'
> > /usr/include/graphviz/gvcint.h:37: error: expected
> > specifier-qualifier-list before 'gvtextlayout_engine_t'
> > /usr/include/graphviz/gvcint.h:91: error: expected
> > specifier-qualifier-list before 'gvevent_key_binding_t'
> > Rgraphviz.c: In function 'getNodeLayouts':
> > Rgraphviz.c:801: error: 'struct <anonymous>' has no member named 'line'
> > Rgraphviz.c:802: error: 'struct <anonymous>' has no member named 'line'
> > Rgraphviz.c:804: error: 'struct <anonymous>' has no member named 'line'
> > Rgraphviz.c:808: error: 'struct <anonymous>' has no member named 'line'
> > Rgraphviz.c: In function 'getEdgeLocs':
> > Rgraphviz.c:930: error: 'struct <anonymous>' has no member named 'line'
> > Rgraphviz.c:941: error: 'struct <anonymous>' has no member named 'line'
> > Rgraphviz.c:945: error: 'struct <anonymous>' has no member named 'line'
> > Rgraphviz.c: In function 'Rgraphviz_graphvizVersion':
> > Rgraphviz.c:986: error: 'GVC_t' has no member named 'info'
> > make: *** [Rgraphviz.o] Error 1
> > chmod: cannot access `/home/CARMA/R/library/Rgraphviz/libs/*': No such
> > file or directory
> > ERROR: compilation failed for package 'Rgraphviz'
> > ** Removing '/home/CARMA/R/library/Rgraphviz'
> >
> >
> > --
> > - Byron C. Wallace
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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> >
>
>


-- 
- Byron C. Wallace