[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.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > 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
>
> [[alternative HTML version deleted]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> <Rgraphviz.log>
More information about the Bioconductor
mailing list