[BioC] Rgraphviz compilation error

Kasper Hansen khanse10 at jhu.edu
Mon Apr 28 04:28:47 CEST 2014 

Vladimir, Venkat, Chong

I believe I have fixed the issue in Rgraphviz 2.9.1, which I just committed.  Source tar balls should be available Tuesday in the development version of Bioconductor.  If some of you could confirm that the issue is fixed, I will back port it to the recent release.

Thanks for the report.  It was a real bug, but manifested itself on Ubuntu due to compiler settings on Ubuntu-12.04 which are more aggressive than normal at flagging (potential) security errors.

Best,
Kasper

On Apr 16, 2014, at 9:23 AM, Venkat Seshan <veseshan at gmail.com> wrote:

> Thanks Kasper & Vladimir. I got the same error with and without system graphviz packages. So the presence of system graphviz packages doesn't make a difference.
> 
> Kasper - Attached is the log from the installation attempt (output of script). The other information you needed are below.
> 
> Thanks,
> Venkat
> 
> ebadmin at ebmaster:~$ gcc --version
> gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
> Copyright (C) 2011 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
> 
> ebadmin at ebmaster:~$ R CMD config CC
> gcc -std=gnu99
> ebadmin at ebmaster:~$ `R CMD config CC` --version
> gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
> Copyright (C) 2011 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
> 
> 
> 
> 
> On Wed, Apr 16, 2014 at 3:44 AM, Kasper Daniel Hansen <khansen at jhsph.edu> wrote:
> 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 at 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 at 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 ‘Rgraphviz’
> >
> > 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.
> >
> > _______________________________________________
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> > Bioconductor at 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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> <Rgraphviz.log>

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