Hi all, I am trying to compile Rgraphiz on Windows 7 64bit with R-2.13.0. I have installed Rtools213.exe from [1]. The 64bit packages in [2] provided me with the 64 bit version of graphviz. After intalling the binary version Rgraphviz 1.30 (in 32bit) it complains (as expected) that:> library(Rgraphviz)Error: package 'Rgraphviz' is not installed for 'arch=x64' I don't understand why the 64 bit version of graphiz is provided but not one for Rgraphviz. Have I missed it somewhere? In any case, it is suggested to build it from source, so I tried following the steps of the README from the source package of Rgraphviz (see below). I have the same error than in [3]. Does anyone know what is going on or if Kasper found a solution back in 2009? thanks in advance, Cheers, Ben C:\BenSave>R --arch x64 CMD build --binary .\Rgraphviz --binary is deprecated * checking for file '.\Rgraphviz/DESCRIPTION' ... OK * preparing 'Rgraphviz': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes ----------------------------------- * installing *source* package 'Rgraphviz' ... Using the following environment variables GRAPHVIZ_INSTALL_DIR=C:\/BenSave\/GoodiesWin64\/graphviz GRAPHVIZ_INSTALL_MAJOR=2 GRAPHVIZ_INSTALL_MINOR=20 GRAPHVIZ_INSTALL_SUBMINOR=3 Using the following compilation and linking flags for Rgraphviz PKG_CPPFLAGS=-IC:\/BenSave\/GoodiesWin64\/graphviz/include/graphviz PKG_LIBS=-LC:\/BenSave\/GoodiesWin64\/graphviz/bin -lgvc-4 -lgraph-4 -lcdt-4 GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 Created file src/Makevars.win Created file R/graphviz_build_version.R ** libs cygwin warning: MS-DOS style path detected: C:/PROGRA~1/R/R-213~1.0/etc/x64/Makeconf Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-213~1.0/etc/x64/Makeco nf CYGWIN environment variable option "nodosfilewarning" turns off this warning. Consult the user's guide for more details about POSIX paths: http://cygwin.com/cygwin-ug-net/using.html#using-pathnames x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c LL_funcs.c -o LL_funcs.o x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c Rgraphviz.c -o Rgraphviz.o x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c RgraphvizInit.c -o RgraphvizInit.o x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c agopen.c -o agopen.o x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c agread.c -o agread.o x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c agwrite.c -o agwrite.o x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c bezier.c -o bezier.o x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c buildEdgeList.c -o buildEdgeList.o x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c buildNodeList.c -o buildNodeList.o x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 -O2 -Wall -std=gnu99 -c doLayout.c -o doLayout.o doLayout.c: In function 'getEdgeLocs': doLayout.c:131:17: error: 'textlabel_t' has no member named 'p' doLayout.c:132:17: error: 'textlabel_t' has no member named 'p' doLayout.c: In function 'getNodeLayouts': doLayout.c:243:13: error: 'textlabel_t' has no member named 'p' doLayout.c:244:13: error: 'textlabel_t' has no member named 'p' make: *** [doLayout.o] Error 1 ERROR: compilation failed for package 'Rgraphviz' * removing 'C:/Users/BVINSO~1/AppData/Local/Temp/Rtmpz6M19V/Rinst76da24d2/Rgraph viz' ----------------------------------- ERROR: package installation failed [1] http://www.murdoch-sutherland.com/Rtools/ [2] http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/ [3] https://stat.ethz.ch/pipermail/bioconductor/2009-March/026585.html
Martin Morgan
2011-May-04 00:01 UTC
[R] Compiling Rgraphiz on Windows 7 64bit with R-2.13.0
On 05/03/2011 03:23 PM, Ben Rhelp wrote:> Hi all, > > I am trying to compile Rgraphiz on Windows 7 64bit with R-2.13.0. I have > installed > > Rtools213.exe from [1]. The 64bit packages in [2] provided me with the 64 bit > version > of graphviz. After intalling the binary version Rgraphviz 1.30 (in 32bit) it > complains (as > > expected) that: >> library(Rgraphviz) > Error: package 'Rgraphviz' is not installed for 'arch=x64' > > I don't understand why the 64 bit version of graphiz is provided but not one for > Rgraphviz. > Have I missed it somewhere? In any case, it is suggested to build it from > source, so I tried > following the steps of the README from the source package of Rgraphviz (see > below). I have the > same error than in [3]. Does anyone know what is going on or if Kasper found a > solution back > > in 2009? > > thanks in advance, > > Cheers, > > Ben > > > C:\BenSave>R --arch x64 CMD build --binary .\Rgraphviz > --binary is deprecated > * checking for file '.\Rgraphviz/DESCRIPTION' ... OK > * preparing 'Rgraphviz': > * checking DESCRIPTION meta-information ... OK > * cleaning src > * installing the package to re-build vignettes > ----------------------------------- > * installing *source* package 'Rgraphviz' ... > Using the following environment variables > GRAPHVIZ_INSTALL_DIR=C:\/BenSave\/GoodiesWin64\/graphviz > GRAPHVIZ_INSTALL_MAJOR=2 > GRAPHVIZ_INSTALL_MINOR=20 > GRAPHVIZ_INSTALL_SUBMINOR=3These should be set to match the version of the graphviz library you're using, MINOR=25 SUBMINOR=20090912.0445> Using the following compilation and linking flags for Rgraphviz > PKG_CPPFLAGS=-IC:\/BenSave\/GoodiesWin64\/graphviz/include/graphviz > PKG_LIBS=-LC:\/BenSave\/GoodiesWin64\/graphviz/bin -lgvc-4 -lgraph-4 -lcdt-4Unfortunately, these will now be incorrect; edit Rgraphviz/configure.win so that the line that includes test ${GRAPHVIZ_INSTALL_MINOR} -eq "21" reads test ${GRAPHVIZ_INSTALL_MINOR} -ge "21" Martin> GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > Created file src/Makevars.win > Created file R/graphviz_build_version.R > ** libs > cygwin warning: > MS-DOS style path detected: C:/PROGRA~1/R/R-213~1.0/etc/x64/Makeconf > Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-213~1.0/etc/x64/Makeco > nf > CYGWIN environment variable option "nodosfilewarning" turns off this warning. > Consult the user's guide for more details about POSIX paths: > http://cygwin.com/cygwin-ug-net/using.html#using-pathnames > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c LL_funcs.c -o LL_funcs.o > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c Rgraphviz.c -o Rgraphviz.o > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c RgraphvizInit.c -o RgraphvizInit.o > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c agopen.c -o agopen.o > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c agread.c -o agread.o > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c agwrite.c -o agwrite.o > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c bezier.c -o bezier.o > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c buildEdgeList.c -o buildEdgeList.o > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c buildNodeList.c -o buildNodeList.o > x86_64-w64-mingw32-gcc -I"C:/PROGRA~1/R/R-213~1.0/include" -IC:/BenSave/GoodiesW > in64/graphviz/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=20 -DWin32 > -O2 -Wall -std=gnu99 -c doLayout.c -o doLayout.o > doLayout.c: In function 'getEdgeLocs': > doLayout.c:131:17: error: 'textlabel_t' has no member named 'p' > doLayout.c:132:17: error: 'textlabel_t' has no member named 'p' > doLayout.c: In function 'getNodeLayouts': > doLayout.c:243:13: error: 'textlabel_t' has no member named 'p' > doLayout.c:244:13: error: 'textlabel_t' has no member named 'p' > make: *** [doLayout.o] Error 1 > ERROR: compilation failed for package 'Rgraphviz' > * removing 'C:/Users/BVINSO~1/AppData/Local/Temp/Rtmpz6M19V/Rinst76da24d2/Rgraph > viz' > ----------------------------------- > ERROR: package installation failed > > > > > [1] http://www.murdoch-sutherland.com/Rtools/ > [2] http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/ > [3] https://stat.ethz.ch/pipermail/bioconductor/2009-March/026585.html > > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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