[BioC] Rgraphviz compilation error

Dan Tenenbaum dtenenba at fhcrc.org
Wed Apr 30 19:31:02 CEST 2014



----- Original Message -----
> From: "Kasper Daniel Hansen" <khansen at jhsph.edu>
> To: "Venkat Seshan" <veseshan at gmail.com>
> Cc: "Chong Tang" <tangc3 at unr.edu>, "Bioconductor mailing list" <bioconductor at r-project.org>, "Kasper Hansen"
> <khanse10 at jhu.edu>
> Sent: Wednesday, April 30, 2014 10:23:52 AM
> Subject: Re: [BioC] Rgraphviz compilation error
> 
> There may be a time lag between submission and building.  The patch
> exists
> in the subversion repos; just checked.
> 


2.9.1 is available via biocLite(); the web page should be updated soon.

Dan


> Best,
> Kasper
> 
> 
> On Wed, Apr 30, 2014 at 11:38 AM, Venkat Seshan <veseshan at gmail.com>
> wrote:
> 
> > http://master.bioconductor.org/packages/devel/bioc/html/Rgraphviz.htmlstill
> > shows 2.9.0
> >
> > Venkat
> >
> >
> > On Tue, Apr 29, 2014 at 4:31 PM, Vladimir Zhurov <vzhurov2 at uwo.ca>
> > wrote:
> >
> > > Kasper,
> > >
> > > Checked out revision 89654 - worked on my workstation.
> > >
> > > Regards.
> > >
> > > Vladimir.
> > >
> > >
> > > On Sun, Apr 27, 2014 at 10:28 PM, Kasper Hansen
> > > <khanse10 at jhu.edu>
> > wrote:
> > >
> > >> 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>
> > >>
> > >>
> > >
> > >
> > > --
> > > 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
> >
> 
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