[BioC] Rgraphviz load problem

Mon Apr 16 22:14:36 CEST 2007

Daniel

When installing from source you need the CRAN compilers. When you  
install R from the .dmg file, you part way through the installation  
routing has the option of clicking "Customize" somewhere along the  
bottom of the screen. That takes you to a screen where you can choose  
to install GCC 4.0.3. Do that! That should give you a directory /usr/ 
local/gcc4.0 which is _required_ for installing R packages from source.

I am _rather_ mystified that you cannot build graphviz from source.  
The error looks strange. My guess is that you need to do
   ./configure
   make
   sudo make install

Anyway, we can try using the binary version. The possible problem is  
that it is compiled using a different compiler than R/Rgrpahviz, so  
you may run into problems. Assuming that the binary version installs  
into /usr/local, you should do

# R CMD INSTALL Rgraphviz_1.13.36.tar.gz --configure-args="--with- 
graphviz=/usr/lcoal"

This should at least get you further than the things below. Drop us  
the output again.

Finally, as Tony is saying, you could opt to go with the Simon's  
Graphviz.

Kasper

On Apr 16, 2007, at 4:00 AM, Daniel Klevebring wrote:

> Hi,
>
> I really appreciate all the help. I'll try to answer the questions
> the best I can:
>
> 0) I went the folder you mentioned and removed traces of "old"
> graphvizes (basically using their "date modified" since I know
> approx. when I installed it)
> 1) I installed R from the CRAN binary, unless the compilers are co-
> installed, then no I haven't. (I have no dir /usr/local/gcc4.0,
> whereis gcc tells me /usr/bin/gcc)
> 2) Yes (R binary from CRAN).
> 3) Default gcc is 4.0.1:
> danielk:~ danielk$ gcc_select
> Current default compiler:
> gcc version 4.0.1 (Apple Computer, Inc. build 5250)
>
> 4) I installed the binary graphviz 2.12. The command line tools (dot,
> neato etc) works perfectly fine:
>
> danielk:~/Desktop danielk$ /usr/local/graphviz-2.12/bin/dot -T gif -o
> kalle2.gif kalle.dot
> where kalle.dot is
> --- kalle.dot ---
> digraph untitled
> 	{
> 		donald -> duck;
> 	}
> --- end kalle.dot ---
>
> 5) Installing Rgraphviz 1.12.3 from source gives the following error:
> danielk:~/Desktop danielk$ R CMD INSTALL Rgraphviz_1.12.3.tar.gz
> * Installing *source* package 'Rgraphviz' ...
> checking for pkg-config... /usr/local/bin/pkg-config
> Package libgvc was not found in the pkg-config search path.
> Perhaps you should add the directory containing `libgvc.pc'
> to the PKG_CONFIG_PATH environment variable
> No package 'libgvc' found
> configure: pkg-config was not able to find graphviz.  Verify graphviz
> is installed and that PKG_CONFIG_PATH is correct.checking for
> dotneato-config... no
> configure: dotneato-config not found in PATH.  Try specifying
> location of graphviz using --with-graphviz
> configure: error: graphviz was not found.
> ERROR: configuration failed for package 'Rgraphviz'
> ** Removing '/Library/Frameworks/R.framework/Versions/2.4/Resources/
> library/Rgraphviz'
>
> 6) Installing Rgraphviz 1.13.36 from BioC Devel gives the following
> error:
> danielk:~/Desktop danielk$ R CMD INSTALL Rgraphviz_1.13.36.tar.gz
> * Installing *source* package 'Rgraphviz' ...
> checking for pkg-config... /usr/local/bin/pkg-config
> Package libgvc was not found in the pkg-config search path.
> Perhaps you should add the directory containing `libgvc.pc'
> to the PKG_CONFIG_PATH environment variable
> No package 'libgvc' found
> configure: pkg-config was not able to find graphviz.  Verify graphviz
> is installed and that PKG_CONFIG_PATH is correct.checking for
> dotneato-config... no
> configure: dotneato-config not found in PATH.  Try specifying
> location of graphviz using --with-graphviz
> configure: error: graphviz was not found.
> ERROR: configuration failed for package 'Rgraphviz'
> ** Removing '/Library/Frameworks/R.framework/Versions/2.4/Resources/
> library/Rgraphviz'
>
> 7) Installing graphviz 2.12 from source using
> $ ./configure
> $ sudo make
>
> danielk:~/Download/graphviz-2.12 danielk$ sudo make
> Password:
> make  all-recursive
> Making all in libltdl
> make  all-am
> Making all in lib
> Making all in cdt
> make[3]: Nothing to be done for `all'.
> Making all in graph
> make[3]: Nothing to be done for `all'.
> Making all in agraph
> make[3]: Nothing to be done for `all'.
> Making all in gd
> if /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -
> I. -I. -I../..  includedir  {cppflags}   -I/usr/local/include  -g -O2
> -fno-common -Wall -DNDEBUG -MT gdtables.lo -MD -MP -MF ".deps/
> gdtables.Tpo" -c -o gdtables.lo gdtables.c; \
> then mv -f ".deps/gdtables.Tpo" ".deps/gdtables.Plo"; else rm -f
> ".deps/gdtables.Tpo"; exit 1; fi
> gcc -DHAVE_CONFIG_H -I. -I. -I../.. includedir "{cppflags}" -I/usr/
> local/include -g -O2 -fno-common -Wall -DNDEBUG -MT gdtables.lo -MD -
> MP -MF .deps/gdtables.Tpo -c gdtables.c  -fno-common -DPIC -o .libs/
> gdtables.o
> i686-apple-darwin8-gcc-4.0.1: includedir: No such file or directory
> i686-apple-darwin8-gcc-4.0.1: {cppflags}: No such file or directory
> make[3]: *** [gdtables.lo] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all] Error 2
>
> So far, the best luck is with the binary graphviz 2.12 Revision 1
> (Intel) from http://www.ryandesign.com/graphviz/ since the command
> line tools work fine.
>
> /daniel
> --
>
> Contact information:
>
> Daniel Klevebring
> M. Sc. Eng., Ph.D. Student
> Dept of Gene Technology
> Royal Institute of Technology, KTH
> SE-106 91 Stockholm, Sweden
>
> Visiting address: Roslagstullsbacken 21, B3
> Delivery address: Roslagsvägen 30B, 104 06, Stockholm
> E-mail: daniel at biotech.kth.se
> E-mail: daniel at arrayadvice.se
> Phone: +46 8 5537 8337 (Office)
> Phone: +46 704 71 65 91 (Mobile)
> Web: http://www.ktharray.se/
> Web: http://www.arrayadvice.se/
> Fax: +46 8 5537 8481
> MSN messenger: klevebring at msn.com
>
>
> On 15 Apr 2007, at 19:51, Kasper Daniel Hansen wrote:
>
>> Daniel
>>
>> By now you may have a bit of a messed up installation of graphviz.
>> As Li, I would like to know the following
>> (1) Have you installed the CRAN compilers? (look for the existence
>> of /usr/local/gcc4.0)
>> (2) I assume you have the CRAN version of R - right?
>> (3) What is your default C compiler
>>  # gcc_select
>> (hopefully it is 4.0)
>> (4) How did you install graphviz
>> (5) And I would like the output of installing Rgraphviz under
>> source (important).
>>
>> You should not have to DYLD_LIBRARY_PATH, indeed it is a bit
>> dangerous to do so under OS X (I am told).
>>
>> If you want to clean up the whole mess, do the following
>> (a) delete all the graphviz versions you have. Perhaps using
>> # make uninstall
>> from you building directory. There are files both in /usr/local/
>> bin, /usr/local/include, /usr/local/lib
>> (b) Install graphviz 2.12 by running configure and make. I have
>> used the CRAN compilers to compile graphviz, just for safety, but I
>> think you can just use the normal gcc (= don't do anything) _if_
>> you are using 4.x
>> (c) Download Rgraphviz from the development version of Bioconductor.
>> (d) Install it by
>> # R CMD INSTALL ....
>>
>> That should work.
>>
>> Kasper
>>
>> On Apr 14, 2007, at 9:35 AM, hpages at fhcrc.org wrote:
>>
>>> Hi Daniel, Seth,
>>>
>>> Quoting Daniel Klevebring <daniel at biotech.kth.se>:
>>>
>>>> After I installed graphviz 2.8 I can't run the command line  
>>>> tools of
>>>> graphviz:
>>>> danielk:~ danielk$ dot
>>>> dyld: Library not loaded: /usr/local/lib/graphviz/libgcc_s. 
>>>> 1.0.dylib
>>>>    Referenced from: /usr/local/lib/graphviz/libgvc.2.dylib
>>>>    Reason: image not found
>>>> Trace/BPT trap
>>>
>>> The graphviz-2.8.dmg available at http://r.research.att.com/
>>> has been broken for months:
>>>   https://stat.ethz.ch/pipermail/r-sig-mac/2007-January/003534.html
>>>
>>> You can "fix" it by adding a symlink to
>>>   /usr/local/gcc4.0/lib/libgcc_s.1.0.dylib
>>> in /usr/local/lib/graphviz/
>>>
>>> (alternatively you can send a friendly reminder to R-SIG-Mac
>>> that graphviz-2.8.dmg is broken)
>>>
>>> Cheers,
>>> H.
>>>
>>> _______________________________________________
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>>
>
>
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