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

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.

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]]