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

Dan Tenenbaum dtenenba at fhcrc.org
Mon Jun 4 08:35:14 CEST 2012 

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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