[BioC] Rgraphviz compilation error
Venkat Seshan
veseshan at gmail.com
Wed Apr 16 15:23:42 CEST 2014
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
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>> >
>>
>>
>>
>> --
>> 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]]
>>
>>
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>
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