Daniel,

Please read Herve's reply to your post and try what he suggests and then see
if you problem still persists. He and I both had problems with graphviz and
his solution worked for both of us in the past.

Tony

On 4/16/07, Daniel Klevebring <daniel@biotech.kth.se> 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@biotech.kth.se
> E-mail: daniel@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@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@fhcrc.org wrote:
> >
> >> Hi Daniel, Seth,
> >>
> >> Quoting Daniel Klevebring <daniel@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.
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives: http://news.gmane.org/
> >> gmane.science.biology.informatics.conductor
> >
>
>
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