[Bioc-devel] Rgraphviz installation: collect2: ld returned 1 exit status
Dan Tenenbaum
dtenenba at fhcrc.org
Mon Jun 4 19:35:40 CEST 2012
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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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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