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

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Mon Jun 4 10:29:13 CEST 2012 

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-wind
>> 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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>
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