What Vladimir suggests should not be necessary, and I am interesting in
looking a bit at this.

The error message Venkat posts is unfortunately completely uninformative.
 What happens during Rgraphviz installation is
  1) The C(++) code of graphviz gets compiled
  2) Rgraphviz gets compiled and linked to (1)

The error message Venkat posts just tells us that (2) fails, which is
usually because (1) fails, but we cannot see this.  I really don't
understand why Vladimir's suggestion of hand-compiling graphviz and then
using --with-graphviz works, because that ought to be essentially what
happens in a standard installation.

I would like the following

(1) The full output of the Rgraphviz installation (yes, I know it is long).
(2) What is the specific version of the C compiler used.
(3) What is the output of
  R CMD config CC
and
  `R CMD config CC` --version

Best,
Kasper



On Wed, Apr 16, 2014 at 5:39 AM, Vladimir Zhurov <vzhurov2@uwo.ca> wrote:

> Venkat,
>
> What you described is an exactly same error that I got today during
> upgrade. My system is also Ubuntu 12.04 (LTS). Also in this particular mode
> of installation system graphviz version is irrelevant as by default
> Rgraphviz is bundled with the slimmed copy of graphviz 2.28. And default
> installation breaks with the gvc.h error. Installation using system
> graphviz of 2.26 or the most recent version (2.38) also did not work though
> with different errors.
>
> What worked for me in the end was to upgrade system graphviz from source to
> exactly 2.28, using just bug patch from Rgraphviz package (as I did not
> want to break system graphviz by slimming it). Then I was able to install
> Rgraphviz using system graphviz.
>
> The whole process is below.
>
> In shell:
>
> # download and unpack graphviz v.2.28 sources
>
> wget
> http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.28.0.tar.gz
> tar xzf graphviz-2.28.0.tar.gz
>
> # download and unpack Rgraphviz source package
>
> wget
>
> http://www.bioconductor.org/packages/release/bioc/src/contrib/Rgraphviz_2.8.0.tar.gz
> tar xzf Rgraphviz_2.8.0.tar.gz
>
> # patch, configure, build and install graphviz
>
> cd ./graphviz-2.28.0/
> patch -p1 <
> ../Rgraphviz/inst/prepare/patches_2.28.0/graphviz-2.28.0-bugs.patch
> ./configure
> make
> sudo make install
>
>
> In R:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("Rgraphviz", configure.args="--with-graphviz") # uses system
> graphviz instead of bundled
>
>
> Hope this helps.
>
> Regards.
>
> Vladimir.
>
>
>
>
>
> On Tue, Apr 15, 2014 at 1:12 PM, Venkat Seshan [guest] <
> guest@bioconductor.org> wrote:
>
> >
> > When updating to Bioconductor 2.14 I get the following error from
> > Rgraphviz.
> >
> > In file included from LL_funcs.c:1:0:
> > common.h:16:17: fatal error: gvc.h: No such file or directory
> > compilation terminated.
> > make: *** [LL_funcs.o] Error 1
> > ERROR: compilation failed for package â€˜Rgraphvizâ€™
> >
> > The server runs Ubuntu 12.04 (LTS) and the necessary packages are
> > available:
> >
> > ii  graphviz                         2.26.3-10ubuntu1.1
> >  rich set of graph drawing tools
> > ii  graphviz-dev                     2.26.3-10ubuntu1.1
> >  transitional package for graphviz-dev rename
> > ii  libgraphviz-dev                  2.26.3-10ubuntu1.1
> >  graphviz libs and headers against which to build applications
> >
> >
> > All the other packages were successfully updated.
> >
> > Thanks,
> > Venkat
> >
> >
> >  -- output of sessionInfo():
> >
> > > sessionInfo()
> > R version 3.1.0 (2014-04-10)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] BiocInstaller_1.14.1
> >
> > loaded via a namespace (and not attached):
> > [1] tools_3.1.0
> >
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>
>
> --
> Dr. Vladimir Zhurov
> Research Associate
> Department of Biology, BGS3051 and WSC339
> University of Western Ontario
> Tel.: 519-661-2111 ext. 86794 and 86467
> Fax: 519-661-3935
> Skype: vzhurov.uwo
>
> http://www.spidermite.org
>
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>
>
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