[Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status

Dan Tenenbaum dtenenba at fhcrc.org
Mon Jun 4 01:19:54 CEST 2012 

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]]
>
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