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Rgraphviz install problem.HELP!!!!!

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Last seen 10.3 years ago

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/Rgrap hviz/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/li bunix/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/Rgrap hviz/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.

Rgraphviz Rgraphviz • 1.9k views

ADD COMMENT • link updated 10.7 years ago by Kasper Hansen ▴ 30 • written 10.7 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2014-04-27

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/Rgr aphviz/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/Rgraphv iz/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/Rgr aphviz/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.