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List: bioconductor
Subject: Re: [BioC] Rgraphviz install problem.HELP!!!!!
From: Kasper Hansen <khanse10 () jhu ! edu>
Date: 2014-04-28 2:29:57
Message-ID: C09FF427-BF12-4D1C-A004-FDFE3160DBB2 () jhu ! edu
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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@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.
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