Kasper, Checked out revision 89654 - worked on my workstation. Regards. Vladimir. On Sun, Apr 27, 2014 at 10:28 PM, Kasper Hansen 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 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 > 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 > 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 ‘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@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 > > > > > > > > -- 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]]