installing Rgraphviz under CentOS 5.6
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 11 weeks ago
United States
Dear list, I met troubles installing Rgraphviz. Could anybody help me to figure this out? R version 2.13.0 (2011-04-13) Error log, $ sudo R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_1.30.1.tar.gz checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E 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 for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for whether compiler has bool... yes configure: Using Graphviz dir '/usr/local' configure: Found Graphviz version '2.28.0'. configure: Graphviz major version is '2' and minor version is '28'. configure: Using the following compilation and linking flags for Rgraphviz configure: PKG_CPPFLAGS=-I/usr/local/include/graphviz configure: PKG_LIBS=-L/usr/local/lib/graphviz -L/usr/local/lib -lgvc configure: GVIZ_DEFS= -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 configure: Setting Graphviz Build version to '2.28.0'. configure: creating ./config.status config.status: creating R/graphviz_build_version.R config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c LL_funcs.c -o LL_funcs.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c Rgraphviz.c -o Rgraphviz.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c agopen.c -o agopen.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c agread.c -o agread.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c agwrite.c -o agwrite.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c bezier.c -o bezier.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c buildEdgeList.c -o buildEdgeList.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c buildNodeList.c -o buildNodeList.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c doLayout.c -o doLayout.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c graphvizVersion.c -o graphvizVersion.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o -L/usr/local/lib/graphviz -L/usr/local/lib -lgvc installing to /usr/local/lib64/R/library/Rgraphviz/libs ** R ** inst ** preparing package for lazy loading Creating a new generic function for "head" in "Rgraphviz" Creating a new generic function for "tail" in "Rgraphviz" Creating a new generic function for "lines" in "Rgraphviz" Creating a new generic function for "plot" in "Rgraphviz" ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: call: value[[3L]](cond) error: unable to load shared object '/usr/local/lib64/R/library/Rgraphviz/libs/Rgraphviz.so': libgvc.so.6: cannot open shared object file: No such file or directory Check that (1) graphviz is installed on your system; (2) the installed version of graphviz matches '2.28.0'; this is the version used to build this Rgraphviz package; (3) graphviz is accessible to R, e.g., the path to the graphviz 'bin' directory is in the system 'PATH' variable. See additional instructions in the 'README' file of the Rgraphviz 'source' distribution, available at http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html Ask further questions on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html Error: loading failed Execution halted ERROR: loading failed Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu
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@kasper-daniel-hansen-2979
Last seen 11 weeks ago
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Is graphviz in your LD_LIBRARY_PATH? Kasper On Tue, Sep 27, 2011 at 3:07 PM, Ou, Jianhong <jianhong.ou at="" umassmed.edu=""> wrote: > Dear list, > > I met troubles installing Rgraphviz. Could anybody help me to figure this out? > > R version 2.13.0 (2011-04-13) > Error log, > > $ sudo R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_1.30.1.tar.gz > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking how to run the C preprocessor... gcc -E > 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 for stdbool.h that conforms to C99... yes > checking for _Bool... yes > checking for whether compiler has bool... yes > configure: Using Graphviz dir '/usr/local' > configure: Found Graphviz version '2.28.0'. > configure: Graphviz major version is '2' and minor version is '28'. > configure: Using the following compilation and linking flags for Rgraphviz > configure: ? ?PKG_CPPFLAGS=-I/usr/local/include/graphviz > configure: ? ?PKG_LIBS=-L/usr/local/lib/graphviz -L/usr/local/lib -lgvc > configure: ? ?GVIZ_DEFS= -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 > configure: Setting Graphviz Build version to '2.28.0'. > configure: creating ./config.status > config.status: creating R/graphviz_build_version.R > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c LL_funcs.c -o LL_funcs.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c Rgraphviz.c -o Rgraphviz.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c RgraphvizInit.c -o RgraphvizInit.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c agopen.c -o agopen.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c agread.c -o agread.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c agwrite.c -o agwrite.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c bezier.c -o bezier.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c buildEdgeList.c -o buildEdgeList.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c buildNodeList.c -o buildNodeList.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c doLayout.c -o doLayout.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c graphvizVersion.c -o graphvizVersion.o > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz ?-DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 ?-I/usr/local/include ? ?-fpic ?-g -O2 -c init.c -o init.o > gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o -L/usr/local/lib/graphviz -L/usr/local/lib -lgvc > installing to /usr/local/lib64/R/library/Rgraphviz/libs > ** R > ** inst > ** preparing package for lazy loading > Creating a new generic function for "head" in "Rgraphviz" > Creating a new generic function for "tail" in "Rgraphviz" > Creating a new generic function for "lines" in "Rgraphviz" > Creating a new generic function for "plot" in "Rgraphviz" > ** help > *** installing help indices > ** building package indices ... > ** testing if installed package can be loaded > Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: > ?call: value[[3L]](cond) > ?error: unable to load shared object '/usr/local/lib64/R/library/Rgraphviz/libs/Rgraphviz.so': > ?libgvc.so.6: cannot open shared object file: No such file or directory > > ?Check that (1) graphviz is installed on your system; (2) the > ?installed version of graphviz matches '2.28.0'; this is the version > ?used to build this Rgraphviz package; (3) graphviz is accessible to > ?R, e.g., the path to the graphviz 'bin' directory is in the system > ?'PATH' variable. ?See additional instructions in the 'README' file of > ?the Rgraphviz 'source' distribution, available at > > ?http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html > > ?Ask further questions on the Bioconductor mailing list > > ?http://bioconductor.org/docs/mailList.html > > > Error: loading failed > Execution halted > ERROR: loading failed > > Yours sincerely, > > Jianhong Ou > > jianhong.ou at umassmed.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi Kasper, I think it is. $ echo $LD_LIBRARY_PATH /usr/local/lib $ ls /usr/local/lib graphviz libcgraph.so libgraph.so.5.0.0 libgvpr.so libpathplan.so.4.0.0 libcdt.la libcgraph.so.6 libgvc.la libgvpr.so.2 libxdot.la libcdt.so libcgraph.so.6.0.0 libgvc.so libgvpr.so.2.0.0 libxdot.so libcdt.so.5 libgraph.la libgvc.so.6 libpathplan.la libxdot.so.4 libcdt.so.5.0.0 libgraph.so libgvc.so.6.0.0 libpathplan.so libxdot.so.4.0.0 libcgraph.la libgraph.so.5 libgvpr.la libpathplan.so.4 pkgconfig $ ls /usr/local/lib/graphviz/ config6 libgvplugin_gd.la libgvplugin_xlib.so go libgvplugin_gd.so libgvplugin_xlib.so.6 guile libgvplugin_gd.so.6 libgvplugin_xlib.so.6.0.0 io libgvplugin_gd.so.6.0.0 lua java libgvplugin_gtk.la ocaml libgvplugin_core.la libgvplugin_gtk.so perl libgvplugin_core.so libgvplugin_gtk.so.6 php libgvplugin_core.so.6 libgvplugin_gtk.so.6.0.0 python libgvplugin_core.so.6.0.0 libgvplugin_neato_layout.la python23 libgvplugin_dot_layout.la libgvplugin_neato_layout.so python24 libgvplugin_dot_layout.so libgvplugin_neato_layout.so.6 python25 libgvplugin_dot_layout.so.6 libgvplugin_neato_layout.so.6.0.0 python26 libgvplugin_dot_layout.so.6.0.0 libgvplugin_pango.la python27 libgvplugin_gdk_pixbuf.la libgvplugin_pango.so R libgvplugin_gdk_pixbuf.so libgvplugin_pango.so.6 ruby libgvplugin_gdk_pixbuf.so.6 libgvplugin_pango.so.6.0.0 sharp libgvplugin_gdk_pixbuf.so.6.0.0 libgvplugin_xlib.la tcl Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Sep 27, 2011, at 3:23 PM, Kasper Daniel Hansen wrote: > Is graphviz in your LD_LIBRARY_PATH? > > Kasper > > On Tue, Sep 27, 2011 at 3:07 PM, Ou, Jianhong <jianhong.ou at="" umassmed.edu=""> wrote: >> Dear list, >> >> I met troubles installing Rgraphviz. Could anybody help me to figure this out? >> >> R version 2.13.0 (2011-04-13) >> Error log, >> >> $ sudo R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_1.30.1.tar.gz >> checking for gcc... gcc >> checking for C compiler default output file name... a.out >> checking whether the C compiler works... yes >> checking whether we are cross compiling... no >> checking for suffix of executables... >> checking for suffix of object files... o >> checking whether we are using the GNU C compiler... yes >> checking whether gcc accepts -g... yes >> checking for gcc option to accept ISO C89... none needed >> checking how to run the C preprocessor... gcc -E >> 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 for stdbool.h that conforms to C99... yes >> checking for _Bool... yes >> checking for whether compiler has bool... yes >> configure: Using Graphviz dir '/usr/local' >> configure: Found Graphviz version '2.28.0'. >> configure: Graphviz major version is '2' and minor version is '28'. >> configure: Using the following compilation and linking flags for Rgraphviz >> configure: PKG_CPPFLAGS=-I/usr/local/include/graphviz >> configure: PKG_LIBS=-L/usr/local/lib/graphviz -L/usr/local/lib -lgvc >> configure: GVIZ_DEFS= -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 >> configure: Setting Graphviz Build version to '2.28.0'. >> configure: creating ./config.status >> config.status: creating R/graphviz_build_version.R >> config.status: creating src/Makevars >> ** libs >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c LL_funcs.c -o LL_funcs.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c Rgraphviz.c -o Rgraphviz.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c agopen.c -o agopen.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c agread.c -o agread.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c agwrite.c -o agwrite.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c bezier.c -o bezier.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c buildEdgeList.c -o buildEdgeList.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c buildNodeList.c -o buildNodeList.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c doLayout.c -o doLayout.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c graphvizVersion.c -o graphvizVersion.o >> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c init.c -o init.o >> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o -L/usr/local/lib/graphviz -L/usr/local/lib -lgvc >> installing to /usr/local/lib64/R/library/Rgraphviz/libs >> ** R >> ** inst >> ** preparing package for lazy loading >> Creating a new generic function for "head" in "Rgraphviz" >> Creating a new generic function for "tail" in "Rgraphviz" >> Creating a new generic function for "lines" in "Rgraphviz" >> Creating a new generic function for "plot" in "Rgraphviz" >> ** help >> *** installing help indices >> ** building package indices ... >> ** testing if installed package can be loaded >> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: >> call: value[[3L]](cond) >> error: unable to load shared object '/usr/local/lib64/R/library/Rgraphviz/libs/Rgraphviz.so': >> libgvc.so.6: cannot open shared object file: No such file or directory >> >> Check that (1) graphviz is installed on your system; (2) the >> installed version of graphviz matches '2.28.0'; this is the version >> used to build this Rgraphviz package; (3) graphviz is accessible to >> R, e.g., the path to the graphviz 'bin' directory is in the system >> 'PATH' variable. See additional instructions in the 'README' file of >> the Rgraphviz 'source' distribution, available at >> >> http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html >> >> Ask further questions on the Bioconductor mailing list >> >> http://bioconductor.org/docs/mailList.html >> >> >> Error: loading failed >> Execution halted >> ERROR: loading failed >> >> Yours sincerely, >> >> Jianhong Ou >> >> jianhong.ou at umassmed.edu >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 11 weeks ago
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Hi Martin, Is everything resolved? $R CMD ldd Rgraphviz/src/Rgraphviz.so linux-vdso.so.1 => (0x00007fffd7f0b000) libgvc.so.6 => /usr/local/lib/libgvc.so.6 (0x00002afd60706000) libc.so.6 => /lib64/libc.so.6 (0x00002afd609a5000) libxdot.so.4 => /usr/local/lib/libxdot.so.4 (0x00002afd60cfd000) libgraph.so.5 => /usr/local/lib/libgraph.so.5 (0x00002afd60f00000) libcdt.so.5 => /usr/local/lib/libcdt.so.5 (0x00002afd6110d000) libpathplan.so.4 => /usr/local/lib/libpathplan.so.4 (0x00002afd61312000) libdl.so.2 => /lib64/libdl.so.2 (0x00002afd6151a000) libexpat.so.0 => /lib64/libexpat.so.0 (0x00002afd6171f000) libz.so.1 => /usr/lib64/libz.so.1 (0x00002afd61941000) libm.so.6 => /lib64/libm.so.6 (0x00002afd61b55000) /lib64/ld-linux-x86-64.so.2 (0x000000349cc00000) Thank you for your time. Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Sep 27, 2011, at 6:09 PM, Martin Morgan wrote: > On 09/27/2011 12:48 PM, Ou, Jianhong wrote: >> Hi Kasper, >> >> I think it is. >> >> $ echo $LD_LIBRARY_PATH >> /usr/local/lib >> >> $ ls /usr/local/lib >> graphviz libcgraph.so libgraph.so.5.0.0 libgvpr.so libpathplan.so.4.0.0 >> libcdt.la libcgraph.so.6 libgvc.la libgvpr.so.2 libxdot.la >> libcdt.so libcgraph.so.6.0.0 libgvc.so libgvpr.so.2.0.0 libxdot.so >> libcdt.so.5 libgraph.la libgvc.so.6 libpathplan.la libxdot.so.4 >> libcdt.so.5.0.0 libgraph.so libgvc.so.6.0.0 libpathplan.so libxdot.so.4.0.0 >> libcgraph.la libgraph.so.5 libgvpr.la libpathplan.so.4 pkgconfig >> >> $ ls /usr/local/lib/graphviz/ >> config6 libgvplugin_gd.la libgvplugin_xlib.so >> go libgvplugin_gd.so libgvplugin_xlib.so.6 >> guile libgvplugin_gd.so.6 libgvplugin_xlib.so.6.0.0 >> io libgvplugin_gd.so.6.0.0 lua >> java libgvplugin_gtk.la ocaml >> libgvplugin_core.la libgvplugin_gtk.so perl >> libgvplugin_core.so libgvplugin_gtk.so.6 php >> libgvplugin_core.so.6 libgvplugin_gtk.so.6.0.0 python >> libgvplugin_core.so.6.0.0 libgvplugin_neato_layout.la python23 >> libgvplugin_dot_layout.la libgvplugin_neato_layout.so python24 >> libgvplugin_dot_layout.so libgvplugin_neato_layout.so.6 python25 >> libgvplugin_dot_layout.so.6 libgvplugin_neato_layout.so.6.0.0 python26 >> libgvplugin_dot_layout.so.6.0.0 libgvplugin_pango.la python27 >> libgvplugin_gdk_pixbuf.la libgvplugin_pango.so R >> libgvplugin_gdk_pixbuf.so libgvplugin_pango.so.6 ruby >> libgvplugin_gdk_pixbuf.so.6 libgvplugin_pango.so.6.0.0 sharp >> libgvplugin_gdk_pixbuf.so.6.0.0 libgvplugin_xlib.la tcl >> >> >> Yours sincerely, >> >> Jianhong Ou >> >> jianhong.ou at umassmed.edu >> >> >> On Sep 27, 2011, at 3:23 PM, Kasper Daniel Hansen wrote: >> >>> Is graphviz in your LD_LIBRARY_PATH? >>> >>> Kasper >>> >>> On Tue, Sep 27, 2011 at 3:07 PM, Ou, Jianhong<jianhong.ou at="" umassmed.edu=""> wrote: >>>> Dear list, >>>> >>>> I met troubles installing Rgraphviz. Could anybody help me to figure this out? >>>> >>>> R version 2.13.0 (2011-04-13) >>>> Error log, >>>> >>>> $ sudo R CMD INSTALL --configure-args='--with- graphviz=/usr/local' Rgraphviz_1.30.1.tar.gz >>>> checking for gcc... gcc >>>> checking for C compiler default output file name... a.out >>>> checking whether the C compiler works... yes >>>> checking whether we are cross compiling... no >>>> checking for suffix of executables... >>>> checking for suffix of object files... o >>>> checking whether we are using the GNU C compiler... yes >>>> checking whether gcc accepts -g... yes >>>> checking for gcc option to accept ISO C89... none needed >>>> checking how to run the C preprocessor... gcc -E >>>> 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 for stdbool.h that conforms to C99... yes >>>> checking for _Bool... yes >>>> checking for whether compiler has bool... yes >>>> configure: Using Graphviz dir '/usr/local' >>>> configure: Found Graphviz version '2.28.0'. >>>> configure: Graphviz major version is '2' and minor version is '28'. >>>> configure: Using the following compilation and linking flags for Rgraphviz >>>> configure: PKG_CPPFLAGS=-I/usr/local/include/graphviz >>>> configure: PKG_LIBS=-L/usr/local/lib/graphviz -L/usr/local/lib -lgvc >>>> configure: GVIZ_DEFS= -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 >>>> configure: Setting Graphviz Build version to '2.28.0'. >>>> configure: creating ./config.status >>>> config.status: creating R/graphviz_build_version.R >>>> config.status: creating src/Makevars >>>> ** libs >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c LL_funcs.c -o LL_funcs.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c Rgraphviz.c -o Rgraphviz.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c RgraphvizInit.c -o RgraphvizInit.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c agopen.c -o agopen.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c agread.c -o agread.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c agwrite.c -o agwrite.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c bezier.c -o bezier.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c buildEdgeList.c -o buildEdgeList.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c buildNodeList.c -o buildNodeList.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c doLayout.c -o doLayout.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c graphvizVersion.c -o graphvizVersion.o >>>> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include/graphviz -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -I/usr/local/include -fpic -g -O2 -c init.c -o init.o >>>> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o -L/usr/local/lib/graphviz -L/usr/local/lib -lgvc > > I guess at this point you have the Rgraphviz.so in Rgraphviz/src. Try > > R CMD ldd Rgraphviz/src/Rgraphviz.so > > to see the libraries Rgraphviz will try to link to. Everything should > resolve. If not it's a system configuration issue, maybe ldconfig > instead of LD_LIBRARY_PATH, maybe permissions on the graphviz libraries, > maybe full path to graphviz directory in LD_LIBRARY_PATH? > > Martin > >>>> installing to /usr/local/lib64/R/library/Rgraphviz/libs >>>> ** R >>>> ** inst >>>> ** preparing package for lazy loading >>>> Creating a new generic function for "head" in "Rgraphviz" >>>> Creating a new generic function for "tail" in "Rgraphviz" >>>> Creating a new generic function for "lines" in "Rgraphviz" >>>> Creating a new generic function for "plot" in "Rgraphviz" >>>> ** help >>>> *** installing help indices >>>> ** building package indices ... >>>> ** testing if installed package can be loaded >>>> Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details: >>>> call: value[[3L]](cond) >>>> error: unable to load shared object '/usr/local/lib64/R/library/Rgraphviz/libs/Rgraphviz.so': >>>> libgvc.so.6: cannot open shared object file: No such file or directory >>>> >>>> Check that (1) graphviz is installed on your system; (2) the >>>> installed version of graphviz matches '2.28.0'; this is the version >>>> used to build this Rgraphviz package; (3) graphviz is accessible to >>>> R, e.g., the path to the graphviz 'bin' directory is in the system >>>> 'PATH' variable. See additional instructions in the 'README' file of >>>> the Rgraphviz 'source' distribution, available at >>>> >>>> http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html >>>> >>>> Ask further questions on the Bioconductor mailing list >>>> >>>> http://bioconductor.org/docs/mailList.html >>>> >>>> >>>> Error: loading failed >>>> Execution halted >>>> ERROR: loading failed >>>> >>>> Yours sincerely, >>>> >>>> Jianhong Ou >>>> >>>> jianhong.ou at umassmed.edu >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 11 weeks ago
United States
$ R CMD ldd /usr/local/lib/libgvc.so.6 linux-vdso.so.1 => (0x00007fff173fc000) libxdot.so.4 => /usr/local/lib/libxdot.so.4 (0x00002b5c100e0000) libgraph.so.5 => /usr/local/lib/libgraph.so.5 (0x00002b5c102e4000) libcdt.so.5 => /usr/local/lib/libcdt.so.5 (0x00002b5c104f0000) libpathplan.so.4 => /usr/local/lib/libpathplan.so.4 (0x00002b5c106f5000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b5c10914000) libexpat.so.0 => /lib64/libexpat.so.0 (0x00002b5c10b18000) libz.so.1 => /usr/lib64/libz.so.1 (0x00002b5c10d3a000) libm.so.6 => /lib64/libm.so.6 (0x00002b5c10f4f000) libc.so.6 => /lib64/libc.so.6 (0x00002b5c111d2000) /lib64/ld-linux-x86-64.so.2 (0x000000349cc00000) $ ls -l /usr/local/lib/libgvc.so.6 lrwxrwxrwx 1 root root 15 Jun 22 11:55 /usr/local/lib/libgvc.so.6 -> libgvc.so.6.0.0 Is that mean I should reinstall the graphiv? Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Sep 28, 2011, at 9:49 AM, Martin Morgan wrote: > ls -l /usr/local/lib/libgvc.so.6
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 11 weeks ago
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Hi Martin, Thans a lots. You are right. The problem is that a system configuration issue. When I tried sudo LD_LIBRARY_PATH=/usr/lib:/usr/local/lib R CMD INSTALL Rgraphviz_1.30.1.tar.gz It works well. However, I should use LD_LIBRARY_PATH=/usr/lib:/usr/local/lib R before I load the Rgraphviz package everytime. I will fix this latter. Thank you very much for your help. Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Sep 28, 2011, at 1:22 PM, Martin Morgan wrote: > On 09/28/2011 09:35 AM, Ou, Jianhong wrote: >> Here is the output, >> >> $dot -V >> dot - graphviz version 2.28.0 (20110621.2140) >> >> $ dot -otestfile >> graph graphname{ >> a -- b -- c; >> b -- d; >> } >> graph graphname { >> node [label="\N"]; >> graph [bb="0,0,126,180"]; >> a [pos="63,162", width="0.75", height="0.5"]; >> b [pos="63,90", width="0.75", height="0.5"]; >> c [pos="27,18", width="0.75", height="0.5"]; >> d [pos="99,18", width="0.75", height="0.5"]; >> a -- b [pos="63,143.7 63,132.85 63,118.92 63,108.1"]; >> b -- c [pos="54.65,72.765 48.835,61.456 41.11,46.437 35.304,35.147"]; >> b -- d [pos="71.35,72.765 77.165,61.456 84.89,46.437 90.696,35.147"]; >> } >> >> >> Yours sincerely, > > I'm really just guess at this point; what about > > sudo R CMD ldd -r > > for Rgraphviz.so and the libraries that are causing problems? > >> >> Jianhong Ou >> >> jianhong.ou at umassmed.edu >> >> >> On Sep 28, 2011, at 12:14 PM, Martin Morgan wrote: >> >>> On 09/28/2011 06:53 AM, Ou, Jianhong wrote: >>>> $ R CMD ldd /usr/local/lib/libgvc.so.6 >>>> linux-vdso.so.1 => (0x00007fff173fc000) >>>> libxdot.so.4 => /usr/local/lib/libxdot.so.4 (0x00002b5c100e0000) >>>> libgraph.so.5 => /usr/local/lib/libgraph.so.5 (0x00002b5c102e4000) >>>> libcdt.so.5 => /usr/local/lib/libcdt.so.5 (0x00002b5c104f0000) >>>> libpathplan.so.4 => /usr/local/lib/libpathplan.so.4 (0x00002b5c106f5000) >>>> libdl.so.2 => /lib64/libdl.so.2 (0x00002b5c10914000) >>>> libexpat.so.0 => /lib64/libexpat.so.0 (0x00002b5c10b18000) >>>> libz.so.1 => /usr/lib64/libz.so.1 (0x00002b5c10d3a000) >>>> libm.so.6 => /lib64/libm.so.6 (0x00002b5c10f4f000) >>>> libc.so.6 => /lib64/libc.so.6 (0x00002b5c111d2000) >>>> /lib64/ld-linux-x86-64.so.2 (0x000000349cc00000) >>>> $ ls -l /usr/local/lib/libgvc.so.6 >>>> lrwxrwxrwx 1 root root 15 Jun 22 11:55 /usr/local/lib/libgvc.so.6 -> libgvc.so.6.0.0 >>>> >>>> Is that mean I should reinstall the graphiv? >>> >>> too hard to tell; sort of looks like you have 64 bit R, 32 bit graphviz >>> and you want 64 bit of each. Does graphviz actually work, e.g., >>> >>> dot --version >>> >>> ? It does not help to truncate the email; I am intentionally not >>> replying to the list to avoid confusing any final resolution. Martin >>> >>>> >>>> Yours sincerely, >>>> >>>> Jianhong Ou >>>> >>>> jianhong.ou at umassmed.edu >>>> >>>> >>>> On Sep 28, 2011, at 9:49 AM, Martin Morgan wrote: >>>> >>>>> ls -l /usr/local/lib/libgvc.so.6 >>>> >>>> >>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 >> >> > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793
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