[BioC] Rgraphviz install problem.HELP!!!!!

leo [guest] guest at bioconductor.org
Wed Apr 16 10:27:59 CEST 2014

I already tried three days to install rgraphviz in bioconductor. This drive me crazy. I searched all the solution in the web without success. I installed all the dependencis and tools under graphviz.org. However, when I install Rgraphviz still cause problem. I wish any expert can help me. I will really appreciate that.

make[3]: *** [ortho.lo] Error 1
make[3]: Leaving directory `/tmp/RtmpSA1s6W/R.INSTALLa327f2d7c85/Rgraphviz/src/graphviz/lib/ortho'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/tmp/RtmpSA1s6W/R.INSTALLa327f2d7c85/Rgraphviz/src/graphviz/lib'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/tmp/RtmpSA1s6W/R.INSTALLa327f2d7c85/Rgraphviz/src/graphviz'
make: *** [install] Error 2
cp: omitting directory `/tmp/RtmpSA1s6W/R.INSTALLa327f2d7c85/Rgraphviz/src/libunix/lib/pkgconfig'
cp: cannot stat `/tmp/RtmpSA1s6W/R.INSTALLa327f2d7c85/Rgraphviz/src/libunix/lib/graphviz/*': No such file or directory
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/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 zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for deflateBound in -lz... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for whether compiler has bool... yes
configure: Using the following compilation and linking flags for Rgraphviz
configure:    PKG_CFLAGS= -I/tmp/RtmpSA1s6W/R.INSTALLa327f2d7c85/Rgraphviz/src/libunix/include/graphviz
configure:    PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz
configure: Compiling using Graphviz version: '2.28.0'.
configure: Using bundled Graphviz: 'TRUE'.
configure: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -I/tmp/RtmpSA1s6W/R.INSTALLa327f2d7c85/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c LL_funcs.c -o LL_funcs.o
In file included from LL_funcs.c:1:0:
common.h:16:17: fatal error: gvc.h: No such file or directory
compilation terminated.
make: *** [LL_funcs.o] Error 1
ERROR: compilation failed for package ‘Rgraphviz’
* removing ‘/home/leochong/R/x86_64-pc-linux-gnu-library/3.1/Rgraphviz’

 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

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