[BioC] Rgraphviz on Fedora Core 6

[Li.Long at isb-sib.ch]

Hi,

I think BioConductor 1.8 goes with R 2.3, BioConductor 1.9 goes with R
2.4.  There are potential compatability issues if you want to mix the
different versions of them...

Apart from that, I would double check if R in your "R CMD INSTALL" is the
same R as your R 2.4.  When they are different, the packages installed
from "CMD INSTALL" will be in different places.  That'll be a possibility
to get what you get.

Li


> 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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>> >
>>
>>
>
>
> --
> - Byron C. Wallace
>