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[Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status
8 messages · J.J.Goeman at lumc.nl, Kasper Daniel Hansen, Dan Tenenbaum
On Sun, Jun 3, 2012 at 12:36 PM, <J.J.Goeman at lumc.nl> wrote:
Hi all, For some time now I am unable to properly R cmd check my own package because I am unable to install the dependency Rgraphviz on my windows 7 64 bit machine. I followed the steps in Rgraphviz's README, but I get an error message when installing Rgraphviz from source that does not mean much to me. I would be grateful if someone could help me out ?by pointing me my mistake and/or the direction of a possible solution.
Download this zip file: http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip Create a directory called c:\graphviz\x64 and unzip the zip file in there so that you have c:\graphviz\x64\bin and so forth. Add c:\graphviz\x64\bin to the end of your PATH environment variable. http://geekswithblogs.net/renso/archive/2009/10/21/how-to-set-the-windows-path-in-windows-7.aspx Dan
Best, Jelle Here's what I did, following the README: - installed latest Rtools 2.15 - installed graphviz 2.28.0 - created environment variables GRAPHVIZ_INSTALL_DIR , GRAPHVIZ_INSTALL_MAJOR &c as README says. - put Rgraphviz's bin directory in my PATH Then I try to install from source, getting the following error(s). SessionInfo below.
source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.6, ?biocLite for help
biocLite("Rgraphviz", type="source")
BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.6. Installing package(s) 'Rgraphviz' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rgraphviz_1.34.0.tar.gz' Content type 'application/x-gzip' length 694533 bytes (678 Kb) opened URL downloaded 678 Kb '\\vf-d5\d5home$\jjgoeman\MyDocs' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. ?Defaulting to Windows directory. * installing *source* package 'Rgraphviz' ... Using the following environment variables GRAPHVIZ_INSTALL_DIR=C:\/R\/Graphviz2.28 GRAPHVIZ_INSTALL_MAJOR=2 GRAPHVIZ_INSTALL_MINOR=28 GRAPHVIZ_INSTALL_SUBMINOR=0 Using the following compilation and linking flags for Rgraphviz ? PKG_CPPFLAGS=-IC:\/R\/Graphviz2.28/include/graphviz ? PKG_LIBS=-LC:\/R\/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 ? GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 Created file src/Makevars.win Created file R/graphviz_build_version.R ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture cygwin warning: ?MS-DOS style path detected: C:/R/R-215~1.0/etc/x64/Makeconf ?Preferred POSIX equivalent is: /cygdrive/c/R/R-215~1.0/etc/x64/Makeconf ?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 gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c LL_funcs.c -o LL_funcs.o LL_funcs.c: In function 'Rgraphviz_agopenSimple': LL_funcs.c:464:29: warning: variable 'curNode' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c Rgraphviz.c -o Rgraphviz.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c agopen.c -o agopen.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c agread.c -o agread.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c agwrite.c -o agwrite.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c bezier.c -o bezier.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c buildEdgeList.c -o buildEdgeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c buildNodeList.c -o buildNodeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c doLayout.c -o doLayout.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c graphvizVersion.c -o graphvizVersion.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ?-I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ?-std=gnu99 -mtune=core2 -c init.c -o init.o gcc -m64 -shared -s -static-libgcc -o Rgraphviz.dll tmp.def 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 -LC:/R/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/R/R-215~1.0/bin/x64 -lR c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lgvc-5 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lgraph-4 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lcdt-4 collect2: ld returned 1 exit status ERROR: compilation failed for package 'Rgraphviz' * removing 'C:/R/R-2.15.0/library/Rgraphviz' * restoring previous 'C:/R/R-2.15.0/library/Rgraphviz' The downloaded source packages are in ? ? ? ? ? ? ? ?'C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm\downloaded_packages' Warning messages: 1: running command 'C:/R/R-215~1.0/bin/x64/R CMD INSTALL -l "C:/R/R-2.15.0/library" ? C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm/downloaded_packages/Rgraphviz_1.34.0.tar.gz' had status 1 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : ?installation of package 'Rgraphviz' had non-zero exit status
sessionInfo()
R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Dutch_Netherlands.1252 ?LC_CTYPE=Dutch_Netherlands.1252 [3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C [5] LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base other attached packages: [1] BiocInstaller_1.4.6 loaded via a namespace (and not attached): [1] tools_2.15.0 ? ? ? ?[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Dear Dan, Thank you very much for your suggestion. I did as you write, but unfortunately I get exactly the same error message(s). Are there any further checks I could do to diagnose? Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 1:20 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status
On Sun, Jun 3, 2012 at 12:36 PM, <J.J.Goeman at lumc.nl> wrote:
Hi all, For some time now I am unable to properly R cmd check my own package because I am unable to install the dependency Rgraphviz on my windows 7 64 bit machine. I followed the steps in Rgraphviz's README, but I get an error message when installing Rgraphviz from source that does not mean much to me. I would be grateful if someone could help me out ?by pointing me my mistake and/or the direction of a possible solution.
Download this zip file: http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip Create a directory called c:\graphviz\x64 and unzip the zip file in there so that you have c:\graphviz\x64\bin and so forth. Add c:\graphviz\x64\bin to the end of your PATH environment variable. http://geekswithblogs.net/renso/archive/2009/10/21/how-to-set-the-windows-path-in-windows-7.aspx Dan
Best, Jelle Here's what I did, following the README: - installed latest Rtools 2.15 - installed graphviz 2.28.0 - created environment variables GRAPHVIZ_INSTALL_DIR , GRAPHVIZ_INSTALL_MAJOR &c as README says. - put Rgraphviz's bin directory in my PATH Then I try to install from source, getting the following error(s). SessionInfo below.
source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.6, ?biocLite for help
biocLite("Rgraphviz", type="source")
BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.6. Installing package(s) 'Rgraphviz' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rgraphviz_1.34.0.tar.gz' Content type 'application/x-gzip' length 694533 bytes (678 Kb) opened URL downloaded 678 Kb '\\vf-d5\d5home$\jjgoeman\MyDocs' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. ?Defaulting to Windows directory. * installing *source* package 'Rgraphviz' ... Using the following environment variables GRAPHVIZ_INSTALL_DIR=C:\/R\/Graphviz2.28 GRAPHVIZ_INSTALL_MAJOR=2 GRAPHVIZ_INSTALL_MINOR=28 GRAPHVIZ_INSTALL_SUBMINOR=0 Using the following compilation and linking flags for Rgraphviz ? PKG_CPPFLAGS=-IC:\/R\/Graphviz2.28/include/graphviz ? PKG_LIBS=-LC:\/R\/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 ? GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 Created file src/Makevars.win Created file R/graphviz_build_version.R ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture cygwin warning: ?MS-DOS style path detected: C:/R/R-215~1.0/etc/x64/Makeconf ?Preferred POSIX equivalent is: /cygdrive/c/R/R-215~1.0/etc/x64/Makeconf ?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 gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c LL_funcs.c -o LL_funcs.o LL_funcs.c: In function 'Rgraphviz_agopenSimple': LL_funcs.c:464:29: warning: variable 'curNode' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c Rgraphviz.c -o Rgraphviz.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c agopen.c -o agopen.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c agread.c -o agread.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c agwrite.c -o agwrite.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c bezier.c -o bezier.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c buildEdgeList.c -o buildEdgeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c buildNodeList.c -o buildNodeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c doLayout.c -o doLayout.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c graphvizVersion.c -o graphvizVersion.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 ? ? -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall ? -std=gnu99 -mtune=core2 -c init.c -o init.o gcc -m64 -shared -s -static-libgcc -o Rgraphviz.dll tmp.def 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 -LC:/R/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/R/R-215~1.0/bin/x64 -lR c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgvc-5 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgraph-4 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lcdt-4 collect2: ld returned 1 exit status ERROR: compilation failed for package 'Rgraphviz' * removing 'C:/R/R-2.15.0/library/Rgraphviz' * restoring previous 'C:/R/R-2.15.0/library/Rgraphviz' The downloaded source packages are in ? ? ? ? ? ? ? ?'C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm\downloaded_packages' Warning messages: 1: running command 'C:/R/R-215~1.0/bin/x64/R CMD INSTALL -l "C:/R/R-2.15.0/library" ? C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm/downloaded_packages/Rg raphviz_1.34.0.tar.gz' had status 1 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : ?installation of package 'Rgraphviz' had non-zero exit status
sessionInfo()
R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Dutch_Netherlands.1252 ?LC_CTYPE=Dutch_Netherlands.1252 [3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C [5] LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base other attached packages: [1] BiocInstaller_1.4.6 loaded via a namespace (and not attached): [1] tools_2.15.0 ? ? ? ?[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
On Sun, Jun 3, 2012 at 11:06 PM, <J.J.Goeman at lumc.nl> wrote:
?Dear Dan, Thank you very much for your suggestion. I did as you write, but unfortunately I get exactly the same error message(s). Are there any further checks I could do to diagnose?
Sorry, I should have been more clear. The instructions I gave were for
installing a binary 64-bit graphviz, you you do not need to install
Rgraphviz from source. You should just be able to:
source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz") ## don't specify type="source"
and now you should be able to R CMD check your package.
Dan
Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 1:20 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status On Sun, Jun 3, 2012 at 12:36 PM, ?<J.J.Goeman at lumc.nl> wrote:
Hi all, For some time now I am unable to properly R cmd check my own package because I am unable to install the dependency Rgraphviz on my windows 7 64 bit machine. I followed the steps in Rgraphviz's README, but I get an error message when installing Rgraphviz from source that does not mean much to me. I would be grateful if someone could help me out ?by pointing me my mistake and/or the direction of a possible solution.
Download this zip file: http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip Create a directory called c:\graphviz\x64 and unzip the zip file in there so that you have c:\graphviz\x64\bin and so forth. Add c:\graphviz\x64\bin to the end of your PATH environment variable. http://geekswithblogs.net/renso/archive/2009/10/21/how-to-set-the-windows-path-in-windows-7.aspx Dan
Best, Jelle Here's what I did, following the README: - installed latest Rtools 2.15 - installed graphviz 2.28.0 - created environment variables GRAPHVIZ_INSTALL_DIR , GRAPHVIZ_INSTALL_MAJOR &c as README says. - put Rgraphviz's bin directory in my PATH Then I try to install from source, getting the following error(s). SessionInfo below.
source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.6, ?biocLite for help
biocLite("Rgraphviz", type="source")
BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.6. Installing package(s) 'Rgraphviz' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rgraphviz_1.34.0.tar.gz' Content type 'application/x-gzip' length 694533 bytes (678 Kb) opened URL downloaded 678 Kb '\\vf-d5\d5home$\jjgoeman\MyDocs' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. ?Defaulting to Windows directory. * installing *source* package 'Rgraphviz' ... Using the following environment variables GRAPHVIZ_INSTALL_DIR=C:\/R\/Graphviz2.28 GRAPHVIZ_INSTALL_MAJOR=2 GRAPHVIZ_INSTALL_MINOR=28 GRAPHVIZ_INSTALL_SUBMINOR=0 Using the following compilation and linking flags for Rgraphviz ? PKG_CPPFLAGS=-IC:\/R\/Graphviz2.28/include/graphviz ? PKG_LIBS=-LC:\/R\/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 ? GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 Created file src/Makevars.win Created file R/graphviz_build_version.R ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture cygwin warning: ?MS-DOS style path detected: C:/R/R-215~1.0/etc/x64/Makeconf ?Preferred POSIX equivalent is: /cygdrive/c/R/R-215~1.0/etc/x64/Makeconf ?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 gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c LL_funcs.c -o LL_funcs.o LL_funcs.c: In function 'Rgraphviz_agopenSimple': LL_funcs.c:464:29: warning: variable 'curNode' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c Rgraphviz.c -o Rgraphviz.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agopen.c -o agopen.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agread.c -o agread.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agwrite.c -o agwrite.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c bezier.c -o bezier.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildEdgeList.c -o buildEdgeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildNodeList.c -o buildNodeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c doLayout.c -o doLayout.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c graphvizVersion.c -o graphvizVersion.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o gcc -m64 -shared -s -static-libgcc -o Rgraphviz.dll tmp.def 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 -LC:/R/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/R/R-215~1.0/bin/x64 -lR c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgvc-5 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgraph-4 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lcdt-4 collect2: ld returned 1 exit status ERROR: compilation failed for package 'Rgraphviz' * removing 'C:/R/R-2.15.0/library/Rgraphviz' * restoring previous 'C:/R/R-2.15.0/library/Rgraphviz' The downloaded source packages are in ? ? ? ? ? ? ? ?'C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm\downloaded_packages' Warning messages: 1: running command 'C:/R/R-215~1.0/bin/x64/R CMD INSTALL -l "C:/R/R-2.15.0/library" C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm/downloaded_packages/Rg raphviz_1.34.0.tar.gz' had status 1 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : ?installation of package 'Rgraphviz' had non-zero exit status
sessionInfo()
R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Dutch_Netherlands.1252 ?LC_CTYPE=Dutch_Netherlands.1252 [3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C [5] LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base other attached packages: [1] BiocInstaller_1.4.6 loaded via a namespace (and not attached): [1] tools_2.15.0 ? ? ? ?[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Hi Dan, That works. Thanks a lot! Is it worthwhile to document this installation option to the README for future users? I'm willing to write. Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 8:35 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status
On Sun, Jun 3, 2012 at 11:06 PM, <J.J.Goeman at lumc.nl> wrote:
?Dear Dan, Thank you very much for your suggestion. I did as you write, but unfortunately I get exactly the same error message(s). Are there any further checks I could do to diagnose?
Sorry, I should have been more clear. The instructions I gave were for installing a binary 64-bit graphviz, you you do not need to install Rgraphviz from source. You should just be able to:
source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz") ## don't specify type="source"
and now you should be able to R CMD check your package.
Dan
Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 1:20 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status On Sun, Jun 3, 2012 at 12:36 PM, ?<J.J.Goeman at lumc.nl> wrote:
Hi all, For some time now I am unable to properly R cmd check my own package because I am unable to install the dependency Rgraphviz on my windows 7 64 bit machine. I followed the steps in Rgraphviz's README, but I get an error message when installing Rgraphviz from source that does not mean much to me. I would be grateful if someone could help me out ?by pointing me my mistake and/or the direction of a possible solution.
Download this zip file: http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip Create a directory called c:\graphviz\x64 and unzip the zip file in there so that you have c:\graphviz\x64\bin and so forth. Add c:\graphviz\x64\bin to the end of your PATH environment variable. http://geekswithblogs.net/renso/archive/2009/10/21/how-to-set-the-wind ows-path-in-windows-7.aspx Dan
Best, Jelle Here's what I did, following the README: - installed latest Rtools 2.15 - installed graphviz 2.28.0 - created environment variables GRAPHVIZ_INSTALL_DIR , GRAPHVIZ_INSTALL_MAJOR &c as README says. - put Rgraphviz's bin directory in my PATH Then I try to install from source, getting the following error(s). SessionInfo below.
source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.6, ?biocLite for help
biocLite("Rgraphviz", type="source")
BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.6. Installing package(s) 'Rgraphviz' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rgraphviz_1.34.0.tar.gz' Content type 'application/x-gzip' length 694533 bytes (678 Kb) opened URL downloaded 678 Kb '\\vf-d5\d5home$\jjgoeman\MyDocs' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. ?Defaulting to Windows directory. * installing *source* package 'Rgraphviz' ... Using the following environment variables GRAPHVIZ_INSTALL_DIR=C:\/R\/Graphviz2.28 GRAPHVIZ_INSTALL_MAJOR=2 GRAPHVIZ_INSTALL_MINOR=28 GRAPHVIZ_INSTALL_SUBMINOR=0 Using the following compilation and linking flags for Rgraphviz ? PKG_CPPFLAGS=-IC:\/R\/Graphviz2.28/include/graphviz ? PKG_LIBS=-LC:\/R\/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 ? GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 Created file src/Makevars.win Created file R/graphviz_build_version.R ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture cygwin warning: ?MS-DOS style path detected: C:/R/R-215~1.0/etc/x64/Makeconf ?Preferred POSIX equivalent is: /cygdrive/c/R/R-215~1.0/etc/x64/Makeconf ?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 gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c LL_funcs.c -o LL_funcs.o LL_funcs.c: In function 'Rgraphviz_agopenSimple': LL_funcs.c:464:29: warning: variable 'curNode' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c Rgraphviz.c -o Rgraphviz.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agopen.c -o agopen.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agread.c -o agread.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agwrite.c -o agwrite.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c bezier.c -o bezier.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildEdgeList.c -o buildEdgeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildNodeList.c -o buildNodeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c doLayout.c -o doLayout.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c graphvizVersion.c -o graphvizVersion.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o gcc -m64 -shared -s -static-libgcc -o Rgraphviz.dll tmp.def 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 -LC:/R/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/R/R-215~1.0/bin/x64 -lR c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgvc-5 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgraph-4 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lcdt-4 collect2: ld returned 1 exit status ERROR: compilation failed for package 'Rgraphviz' * removing 'C:/R/R-2.15.0/library/Rgraphviz' * restoring previous 'C:/R/R-2.15.0/library/Rgraphviz' The downloaded source packages are in ? ? ? ? ? ? ? ?'C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm\downloaded_packages' Warning messages: 1: running command 'C:/R/R-215~1.0/bin/x64/R CMD INSTALL -l "C:/R/R-2.15.0/library" C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm/downloaded_packages/R g raphviz_1.34.0.tar.gz' had status 1 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : ?installation of package 'Rgraphviz' had non-zero exit status
sessionInfo()
R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Dutch_Netherlands.1252 ? LC_CTYPE=Dutch_Netherlands.1252 [3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C [5] LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base other attached packages: [1] BiocInstaller_1.4.6 loaded via a namespace (and not attached): [1] tools_2.15.0 ? ? ? ?[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Yes, it is very worthwhile to do so. Kasper
On Mon, Jun 4, 2012 at 9:47 AM, <J.J.Goeman at lumc.nl> wrote:
?Hi Dan, That works. Thanks a lot! Is it worthwhile to document this installation option to the README for future users? I'm willing to write. Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 8:35 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status On Sun, Jun 3, 2012 at 11:06 PM, ?<J.J.Goeman at lumc.nl> wrote:
?Dear Dan, Thank you very much for your suggestion. I did as you write, but unfortunately I get exactly the same error message(s). Are there any further checks I could do to diagnose?
Sorry, I should have been more clear. The instructions I gave were for installing a binary 64-bit graphviz, you you do not need to install Rgraphviz from source. You should just be able to:
source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz") ## don't specify type="source"
and now you should be able to R CMD check your package.
Dan
Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 1:20 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status On Sun, Jun 3, 2012 at 12:36 PM, ?<J.J.Goeman at lumc.nl> wrote:
Hi all, For some time now I am unable to properly R cmd check my own package because I am unable to install the dependency Rgraphviz on my windows 7 64 bit machine. I followed the steps in Rgraphviz's README, but I get an error message when installing Rgraphviz from source that does not mean much to me. I would be grateful if someone could help me out ?by pointing me my mistake and/or the direction of a possible solution.
Download this zip file: http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip Create a directory called c:\graphviz\x64 and unzip the zip file in there so that you have c:\graphviz\x64\bin and so forth. Add c:\graphviz\x64\bin to the end of your PATH environment variable. http://geekswithblogs.net/renso/archive/2009/10/21/how-to-set-the-wind ows-path-in-windows-7.aspx Dan
Best, Jelle Here's what I did, following the README: - installed latest Rtools 2.15 - installed graphviz 2.28.0 - created environment variables GRAPHVIZ_INSTALL_DIR , GRAPHVIZ_INSTALL_MAJOR &c as README says. - put Rgraphviz's bin directory in my PATH Then I try to install from source, getting the following error(s). SessionInfo below.
source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.6, ?biocLite for help
biocLite("Rgraphviz", type="source")
BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.6. Installing package(s) 'Rgraphviz' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rgraphviz_1.34.0.tar.gz' Content type 'application/x-gzip' length 694533 bytes (678 Kb) opened URL downloaded 678 Kb '\\vf-d5\d5home$\jjgoeman\MyDocs' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. ?Defaulting to Windows directory. * installing *source* package 'Rgraphviz' ... Using the following environment variables GRAPHVIZ_INSTALL_DIR=C:\/R\/Graphviz2.28 GRAPHVIZ_INSTALL_MAJOR=2 GRAPHVIZ_INSTALL_MINOR=28 GRAPHVIZ_INSTALL_SUBMINOR=0 Using the following compilation and linking flags for Rgraphviz ? PKG_CPPFLAGS=-IC:\/R\/Graphviz2.28/include/graphviz ? PKG_LIBS=-LC:\/R\/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 ? GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 Created file src/Makevars.win Created file R/graphviz_build_version.R ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture cygwin warning: ?MS-DOS style path detected: C:/R/R-215~1.0/etc/x64/Makeconf ?Preferred POSIX equivalent is: /cygdrive/c/R/R-215~1.0/etc/x64/Makeconf ?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 gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c LL_funcs.c -o LL_funcs.o LL_funcs.c: In function 'Rgraphviz_agopenSimple': LL_funcs.c:464:29: warning: variable 'curNode' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c Rgraphviz.c -o Rgraphviz.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agopen.c -o agopen.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agread.c -o agread.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agwrite.c -o agwrite.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c bezier.c -o bezier.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildEdgeList.c -o buildEdgeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildNodeList.c -o buildNodeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c doLayout.c -o doLayout.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c graphvizVersion.c -o graphvizVersion.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o gcc -m64 -shared -s -static-libgcc -o Rgraphviz.dll tmp.def 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 -LC:/R/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/R/R-215~1.0/bin/x64 -lR c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgvc-5 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgraph-4 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lcdt-4 collect2: ld returned 1 exit status ERROR: compilation failed for package 'Rgraphviz' * removing 'C:/R/R-2.15.0/library/Rgraphviz' * restoring previous 'C:/R/R-2.15.0/library/Rgraphviz' The downloaded source packages are in ? ? ? ? ? ? ? ?'C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm\downloaded_packages' Warning messages: 1: running command 'C:/R/R-215~1.0/bin/x64/R CMD INSTALL -l "C:/R/R-2.15.0/library" C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm/downloaded_packages/R g raphviz_1.34.0.tar.gz' had status 1 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : ?installation of package 'Rgraphviz' had non-zero exit status
sessionInfo()
R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 [3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C [5] LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base other attached packages: [1] BiocInstaller_1.4.6 loaded via a namespace (and not attached): [1] tools_2.15.0 ? ? ? ?[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Dear Dan and Kasper, I've attached an updated Rgraphviz README with added 64 bit windows section. Best, Jelle -----Original Message----- From: Kasper Daniel Hansen [mailto:kasperdanielhansen at gmail.com] Sent: maandag 4 juni 2012 10:29 To: Goeman, J.J. (MSTAT) Cc: dtenenba at fhcrc.org; bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status Yes, it is very worthwhile to do so. Kasper
On Mon, Jun 4, 2012 at 9:47 AM, <J.J.Goeman at lumc.nl> wrote:
?Hi Dan, That works. Thanks a lot! Is it worthwhile to document this installation option to the README for future users? I'm willing to write. Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 8:35 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status On Sun, Jun 3, 2012 at 11:06 PM, ?<J.J.Goeman at lumc.nl> wrote:
?Dear Dan, Thank you very much for your suggestion. I did as you write, but unfortunately I get exactly the same error message(s). Are there any further checks I could do to diagnose?
Sorry, I should have been more clear. The instructions I gave were for installing a binary 64-bit graphviz, you you do not need to install Rgraphviz from source. You should just be able to:
source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz") ## don't specify type="source"
and now you should be able to R CMD check your package.
Dan
Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 1:20 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status On Sun, Jun 3, 2012 at 12:36 PM, ?<J.J.Goeman at lumc.nl> wrote:
Hi all, For some time now I am unable to properly R cmd check my own package because I am unable to install the dependency Rgraphviz on my windows 7 64 bit machine. I followed the steps in Rgraphviz's README, but I get an error message when installing Rgraphviz from source that does not mean much to me. I would be grateful if someone could help me out ?by pointing me my mistake and/or the direction of a possible solution.
Download this zip file: http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip Create a directory called c:\graphviz\x64 and unzip the zip file in there so that you have c:\graphviz\x64\bin and so forth. Add c:\graphviz\x64\bin to the end of your PATH environment variable. http://geekswithblogs.net/renso/archive/2009/10/21/how-to-set-the-win d ows-path-in-windows-7.aspx Dan
Best, Jelle Here's what I did, following the README: - installed latest Rtools 2.15 - installed graphviz 2.28.0 - created environment variables GRAPHVIZ_INSTALL_DIR , GRAPHVIZ_INSTALL_MAJOR &c as README says. - put Rgraphviz's bin directory in my PATH Then I try to install from source, getting the following error(s). SessionInfo below.
source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.6, ?biocLite for help
biocLite("Rgraphviz", type="source")
BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.6. Installing package(s) 'Rgraphviz' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rgraphviz_1.34.0.tar.gz' Content type 'application/x-gzip' length 694533 bytes (678 Kb) opened URL downloaded 678 Kb '\\vf-d5\d5home$\jjgoeman\MyDocs' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. ?Defaulting to Windows directory. * installing *source* package 'Rgraphviz' ... Using the following environment variables GRAPHVIZ_INSTALL_DIR=C:\/R\/Graphviz2.28 GRAPHVIZ_INSTALL_MAJOR=2 GRAPHVIZ_INSTALL_MINOR=28 GRAPHVIZ_INSTALL_SUBMINOR=0 Using the following compilation and linking flags for Rgraphviz ? PKG_CPPFLAGS=-IC:\/R\/Graphviz2.28/include/graphviz ? PKG_LIBS=-LC:\/R\/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 ? GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 Created file src/Makevars.win Created file R/graphviz_build_version.R ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture cygwin warning: ?MS-DOS style path detected: C:/R/R-215~1.0/etc/x64/Makeconf ?Preferred POSIX equivalent is: /cygdrive/c/R/R-215~1.0/etc/x64/Makeconf ?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 gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c LL_funcs.c -o LL_funcs.o LL_funcs.c: In function 'Rgraphviz_agopenSimple': LL_funcs.c:464:29: warning: variable 'curNode' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c Rgraphviz.c -o Rgraphviz.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agopen.c -o agopen.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agread.c -o agread.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agwrite.c -o agwrite.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c bezier.c -o bezier.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildEdgeList.c -o buildEdgeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildNodeList.c -o buildNodeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c doLayout.c -o doLayout.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c graphvizVersion.c -o graphvizVersion.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o gcc -m64 -shared -s -static-libgcc -o Rgraphviz.dll tmp.def 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 -LC:/R/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/R/R-215~1.0/bin/x64 -lR c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgvc-5 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgraph-4 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lcdt-4 collect2: ld returned 1 exit status ERROR: compilation failed for package 'Rgraphviz' * removing 'C:/R/R-2.15.0/library/Rgraphviz' * restoring previous 'C:/R/R-2.15.0/library/Rgraphviz' The downloaded source packages are in ? ? ? ? ? ? ? ?'C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm\downloaded_packages' Warning messages: 1: running command 'C:/R/R-215~1.0/bin/x64/R CMD INSTALL -l "C:/R/R-2.15.0/library" C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm/downloaded_packages/ R g raphviz_1.34.0.tar.gz' had status 1 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : ?installation of package 'Rgraphviz' had non-zero exit status
sessionInfo()
R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 [3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C [5] LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base other attached packages: [1] BiocInstaller_1.4.6 loaded via a namespace (and not attached): [1] tools_2.15.0 ? ? ? ?[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Hi Jelle,
On Mon, Jun 4, 2012 at 6:13 AM, <J.J.Goeman at lumc.nl> wrote:
?Dear Dan and Kasper, I've attached an updated Rgraphviz README with added 64 bit windows section.
Thanks very much for your contribution. I've added it (with some edits) to Rgraphviz 1.34.1 (release) and 1.35.2 (devel). Dan
Best, Jelle -----Original Message----- From: Kasper Daniel Hansen [mailto:kasperdanielhansen at gmail.com] Sent: maandag 4 juni 2012 10:29 To: Goeman, J.J. (MSTAT) Cc: dtenenba at fhcrc.org; bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status Yes, it is very worthwhile to do so. Kasper On Mon, Jun 4, 2012 at 9:47 AM, ?<J.J.Goeman at lumc.nl> wrote:
?Hi Dan, That works. Thanks a lot! Is it worthwhile to document this installation option to the README for future users? I'm willing to write. Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 8:35 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status On Sun, Jun 3, 2012 at 11:06 PM, ?<J.J.Goeman at lumc.nl> wrote:
?Dear Dan, Thank you very much for your suggestion. I did as you write, but unfortunately I get exactly the same error message(s). Are there any further checks I could do to diagnose?
Sorry, I should have been more clear. The instructions I gave were for installing a binary 64-bit graphviz, you you do not need to install Rgraphviz from source. You should just be able to:
source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz") ## don't specify type="source"
and now you should be able to R CMD check your package.
Dan
Best, Jelle -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] Sent: maandag 4 juni 2012 1:20 To: Goeman, J.J. (MSTAT) Cc: bioc-devel at r-project.org Subject: Re: [Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status On Sun, Jun 3, 2012 at 12:36 PM, ?<J.J.Goeman at lumc.nl> wrote:
Hi all, For some time now I am unable to properly R cmd check my own package because I am unable to install the dependency Rgraphviz on my windows 7 64 bit machine. I followed the steps in Rgraphviz's README, but I get an error message when installing Rgraphviz from source that does not mean much to me. I would be grateful if someone could help me out ?by pointing me my mistake and/or the direction of a possible solution.
Download this zip file: http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/graphviz64.zip Create a directory called c:\graphviz\x64 and unzip the zip file in there so that you have c:\graphviz\x64\bin and so forth. Add c:\graphviz\x64\bin to the end of your PATH environment variable. http://geekswithblogs.net/renso/archive/2009/10/21/how-to-set-the-win d ows-path-in-windows-7.aspx Dan
Best, Jelle Here's what I did, following the README: - installed latest Rtools 2.15 - installed graphviz 2.28.0 - created environment variables GRAPHVIZ_INSTALL_DIR , GRAPHVIZ_INSTALL_MAJOR &c as README says. - put Rgraphviz's bin directory in my PATH Then I try to install from source, getting the following error(s). SessionInfo below.
source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.4.6, ?biocLite for help
biocLite("Rgraphviz", type="source")
BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.6. Installing package(s) 'Rgraphviz' trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/Rgraphviz_1.34.0.tar.gz' Content type 'application/x-gzip' length 694533 bytes (678 Kb) opened URL downloaded 678 Kb '\\vf-d5\d5home$\jjgoeman\MyDocs' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. ?Defaulting to Windows directory. * installing *source* package 'Rgraphviz' ... Using the following environment variables GRAPHVIZ_INSTALL_DIR=C:\/R\/Graphviz2.28 GRAPHVIZ_INSTALL_MAJOR=2 GRAPHVIZ_INSTALL_MINOR=28 GRAPHVIZ_INSTALL_SUBMINOR=0 Using the following compilation and linking flags for Rgraphviz ? PKG_CPPFLAGS=-IC:\/R\/Graphviz2.28/include/graphviz ? PKG_LIBS=-LC:\/R\/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 ? GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 Created file src/Makevars.win Created file R/graphviz_build_version.R ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture cygwin warning: ?MS-DOS style path detected: C:/R/R-215~1.0/etc/x64/Makeconf ?Preferred POSIX equivalent is: /cygdrive/c/R/R-215~1.0/etc/x64/Makeconf ?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 gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c LL_funcs.c -o LL_funcs.o LL_funcs.c: In function 'Rgraphviz_agopenSimple': LL_funcs.c:464:29: warning: variable 'curNode' set but not used [-Wunused-but-set-variable] gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c Rgraphviz.c -o Rgraphviz.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agopen.c -o agopen.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agread.c -o agread.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c agwrite.c -o agwrite.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c bezier.c -o bezier.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildEdgeList.c -o buildEdgeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c buildNodeList.c -o buildNodeList.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c doLayout.c -o doLayout.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c graphvizVersion.c -o graphvizVersion.o gcc -m64 -I"C:/R/R-215~1.0/include" -DNDEBUG -IC:/R/Graphviz2.28/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DWin32 -I"d:/RCompile/CRANpkg/extralibs64/local/include" ? ? -O2 -Wall -std=gnu99 -mtune=core2 -c init.c -o init.o gcc -m64 -shared -s -static-libgcc -o Rgraphviz.dll tmp.def 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 -LC:/R/Graphviz2.28/bin -lgvc-5 -lgraph-4 -lcdt-4 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/R/R-215~1.0/bin/x64 -lR c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgvc-5 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lgraph-4 c:/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../. ./i686-w64-mingw32/bin/ld.exe: cannot find -lcdt-4 collect2: ld returned 1 exit status ERROR: compilation failed for package 'Rgraphviz' * removing 'C:/R/R-2.15.0/library/Rgraphviz' * restoring previous 'C:/R/R-2.15.0/library/Rgraphviz' The downloaded source packages are in ? ? ? ? ? ? ? ?'C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm\downloaded_packages' Warning messages: 1: running command 'C:/R/R-215~1.0/bin/x64/R CMD INSTALL -l "C:/R/R-2.15.0/library" C:\Users\jjgoeman\AppData\Local\Temp\RtmpIH0nAm/downloaded_packages/ R g raphviz_1.34.0.tar.gz' had status 1 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : ?installation of package 'Rgraphviz' had non-zero exit status
sessionInfo()
R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252 [3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C [5] LC_TIME=Dutch_Netherlands.1252 attached base packages: [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base other attached packages: [1] BiocInstaller_1.4.6 loaded via a namespace (and not attached): [1] tools_2.15.0 ? ? ? ?[[alternative HTML version deleted]]
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