Hi there,
I'm having a little trouble installing the devel version of Rgraphviz (release version installs fine for me). I've seen posts from this spring reporting a similar error (common.h:16:17: fatal error: gvc.h: No such file or directory), but it looked like that issue had been solved.
It's possible there's something unusual about my R installation that's causing problems (I installed b it myself in my user directory, not system-wide, and I confess I'm an ignorant sysadmin. I've also got parallel R installations to let me use the release or devel packages, but this hasn't caused me any trouble in the past).
I've tried biocLite, as well as trying to install from command line via R CMD INSTALL, using a tar.gz of Rgraphviz I downloaded from github - same issue with that.
I did this:
source("http://www.bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
Here's the end of the output (session info and uname output are also below):
configure: Using the following compilation and linking flags for Rgraphviz
configure: PKG_CFLAGS= -I/tmp/Rtmp0neKAH/R.INSTALL3b204df0edc8/Rgraphviz/src/libunix/include/graphviz
configure: PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz
configure: GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1
configure: Compiling using Graphviz version: '2.28.0'.
configure: Using bundled Graphviz: 'TRUE'.
configure: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/jayoung/malik_lab_shared/linux_gizmo/lib/Rdevel/R/include -DNDEBUG -I/usr/local/include -I/tmp/Rtmp0neKAH/R.INSTALL3b204df0edc8/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -c LL_funcs.c -o LL_funcs.o
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’
sessionInfo()
R version 3.1.1 Patched (2014-08-07 r66321)
Platform: x86_64-unknown-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_1.15.5
loaded via a namespace (and not attached):
[1] tools_3.1.1
system("uname -a")
Linux gizmod17 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Hmm - any clues? Not sure if this is a bug, or something wrong with my R installation, or maybe LIBRARY or INCLUDE settings. But I thought Rgraphviz was a bundled graphviz library files, so hopefully whatever other libraries I do or don't have installed won't interfere with this installation.
thanks in advance for any help,
Janet Young
Hi there,
Thanks, Kasper - the full output is below.
thanks,
Janet
> biocLite('Rgraphviz')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1.
Installing package(s) 'Rgraphviz'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/Rgraphviz_2.9.1.tar.gz'
Content type 'application/x-gzip' length 7452931 bytes (7.1 Mb)
opened URL
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downloaded 7.1 Mb