[BioC] Regarding Rgraphviz compilation error

[Saurin Jani]

Hi Jeff,

More output of Rgraphviz compilation error:


$ R CMD INSTALL -l /usr/local/lib/R/library
Rgraphviz_1.4.23.tar.gz

I get : --------------------------------

* Installing *source* package 'Rgraphviz' ...
checking for graphviz... checking for
dotneato-config... /usr/bin/dotneato-config
/usr/bin/dotneato-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/local/lib/R/include -I/usr/include/graphviz
-DGRAPHVIZ_1_12 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g -O2 -c
Rgraphviz.c -o Rgraphviz.o
In file included from
/usr/include/graphviz/render.h:49,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/include/graphviz/macros.h:28:1: warning: "NEW"
redefined
In file included from common.h:13,
                 from Rgraphviz.c:1:
/usr/local/lib/R/include/Rdefines.h:129:1: warning:
this is the location of the previous definition
In file included from
/usr/include/graphviz/types.h:11,
                 from
/usr/include/graphviz/render.h:51,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/include/graphviz/pathplan.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/pathplan.h:16,
                 from
/usr/include/graphviz/types.h:11,
                 from
/usr/include/graphviz/render.h:51,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/include/graphviz/pathgeom.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/render.h:52,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/include/graphviz/graph.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/render.h:55,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/include/graphviz/gvrender.h:12: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/gvrender.h:19,
                 from
/usr/include/graphviz/render.h:55,
                 from common.h:22,
                 from Rgraphviz.c:1:
/usr/include/graphviz/gvrenderint.h:12: warning:
ignoring #pragma prototyped
In file included from common.h:23,
                 from Rgraphviz.c:1:
/usr/include/graphviz/graph.h:11: warning: ignoring
#pragma prototyped
In file included from common.h:26,
                 from Rgraphviz.c:1:
/usr/include/graphviz/adjust.h:11: warning: ignoring
#pragma prototyped
In file included from common.h:28,
                 from Rgraphviz.c:1:
/usr/include/graphviz/gvrender.h:12: warning: ignoring
#pragma prototyped
gcc -I/usr/local/lib/R/include -I/usr/include/graphviz
-DGRAPHVIZ_1_12 -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g -O2 -c
RgraphvizInit.c -o RgraphvizInit.o
In file included from
/usr/include/graphviz/render.h:49,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/include/graphviz/macros.h:28:1: warning: "NEW"
redefined
In file included from common.h:13,
                 from RgraphvizInit.c:1:
/usr/local/lib/R/include/Rdefines.h:129:1: warning:
this is the location of the previous definition
In file included from
/usr/include/graphviz/types.h:11,
                 from
/usr/include/graphviz/render.h:51,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/include/graphviz/pathplan.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/pathplan.h:16,
                 from
/usr/include/graphviz/types.h:11,
                 from
/usr/include/graphviz/render.h:51,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/include/graphviz/pathgeom.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/render.h:52,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/include/graphviz/graph.h:11: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/render.h:55,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/include/graphviz/gvrender.h:12: warning: ignoring
#pragma prototyped
In file included from
/usr/include/graphviz/gvrender.h:19,
                 from
/usr/include/graphviz/render.h:55,
                 from common.h:22,
                 from RgraphvizInit.c:1:
/usr/include/graphviz/gvrenderint.h:12: warning:
ignoring #pragma prototyped
In file included from common.h:23,
                 from RgraphvizInit.c:1:
/usr/include/graphviz/graph.h:11: warning: ignoring
#pragma prototyped
In file included from common.h:26,
                 from RgraphvizInit.c:1:
/usr/include/graphviz/adjust.h:11: warning: ignoring
#pragma prototyped
In file included from common.h:28,
                 from RgraphvizInit.c:1:
/usr/include/graphviz/gvrender.h:12: warning: ignoring
#pragma prototyped
common.h:33: warning: `gvc' defined but not used
gcc -shared -L/usr/local/lib -o Rgraphviz.so
Rgraphviz.o RgraphvizInit.o -Wl -L/usr/lib/graphviz
-ldotneato -lm
/usr/bin/ld: cannot find -ldotneato
collect2: ld returned 1 exit status
make: *** [Rgraphviz.so] Error 1
ERROR: compilation failed for package 'Rgraphviz'
** Removing '/usr/local/lib/R/library/Rgraphviz'

---------------------------------------------

Please let me know...

Thank you,
Saurin








--- Jeff Gentry <jgentry at jimmy.harvard.edu> wrote:

> > R CMD INSTALL -l /usr/local/lib/R/library
> > Rgraphviz_1.4.23.tar.gz
> > 
> > get get:
> > ERROR: compilation failed for package 'Rgraphviz'
> 
> Would you like to include just a *little* more of
> the output?
> 
> Thanks
> -J
> 
> 



		
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