[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-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]]
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