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

?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


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