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

[Kasper Hansen]

Are you on Ubuntu, then the bug may be fixed?  See recent reply to another thread on Bioc.

Best,
Kasper

On Apr 16, 2014, at 4:27 AM, leo [guest] <guest at bioconductor.org> wrote:

> 
> Hello,
> 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:    GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1
> 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)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
> [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.