Rgraphviz compilation error
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@kasper-daniel-hansen-2979
Last seen 11 weeks ago
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Committed to release branch as well. On Wed, Apr 30, 2014 at 1:51 PM, Venkat Seshan <veseshan@gmail.com> wrote: > Kasper: > > I too can confirm that 2.9.1 compiles on my server. Thanks, > > Venkat > > > On Wed, Apr 30, 2014 at 1:23 PM, Kasper Daniel Hansen <khansen@jhsph.edu> >wrote: > > > There may be a time lag between submission and building. The patch > exists > > in the subversion repos; just checked. > > > > Best, > > Kasper > > > > > > On Wed, Apr 30, 2014 at 11:38 AM, Venkat Seshan <veseshan@gmail.com> >wrote: > > > >> > >> > http://master.bioconductor.org/packages/devel/bioc/html/Rgraphviz.ht mlstill > >> > >> shows 2.9.0 > >> > >> Venkat > >> > >> > >> On Tue, Apr 29, 2014 at 4:31 PM, Vladimir Zhurov <vzhurov2@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@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@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@ebmaster:~$gcc --version > >> >> > gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 > >> >> > Copyright (C) 2011 Free Software Foundation, Inc. > >> >> > This is free software; see the source for copying conditions. > There > >> is > >> >> NO > >> >> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR > >> >> PURPOSE. > >> >> > > >> >> > ebadmin@ebmaster:~$ R CMD config CC > >> >> > gcc -std=gnu99 > >> >> > ebadmin@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@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@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/Rgraph viz_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 Ã¢â¬ËRgraphvizÃ¢â¬â¢ > >> >> > > > >> >> > > 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 > >> >> > > >> >> > [[alternative HTML version deleted]] > >> >> > > >> >> > > >> >> > _______________________________________________ > >> >> > 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 > >> >> > > >> >> > > >> >> > <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@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
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