[BioC] RGraphiz installation keeps on failing ubuntu 12.04 LTS server

Frederiek - Maarten Kerckhof [guest] guest at bioconductor.org
Mon Apr 28 20:09:11 CEST 2014


I am currently trying to install the bioconductor package 'flowStats' which depends upon the bioconductor package 'Rgraphviz'. As I understand from the Rgraphviz github there may be some issues with getting it installed on 12.04 which should be fixed by using the bundled Graphviz. However I keep on getting the same issues even when using install_github from the devtools package, stating gvc.h: No such file or directory. Which is very weird, as gvc.h can be found (find / -iname gvc.h) in the usr/local/include/graphviz directory. On the other hand, when using the local graphviz installation by R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_*.tar.gz I get the following output, that I cannot seem to understand:

 configure: Using external Graphviz.
 configure: Using Graphviz dir '/usr/local'
 configure: Found Graphviz version '2.38.0'.
 configure: Graphviz major version is '2' and minor version is '38'.
 checking for stdbool.h that conforms to C99... no
 checking for _Bool... no
 checking for whether compiler has bool... no
 configure: Using the following compilation and linking flags for Rgraphviz
 configure:    PKG_CFLAGS=-I/usr/local/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=38
 configure:    PKG_LIBS=-L/usr/local/lib/graphviz -L/usr/local/lib -lgvc
 configure:    GVIZ_DEFS=
 configure: Compiling using Graphviz version: '2.38.0'.
 configure: Using bundled Graphviz: 'FALSE'.
 configure: creating ./config.status
 config.status: creating R/graphviz_build_version.R
 config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG     -I/usr/local/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=38  -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c LL_funcs.c -o LL_funcs.o
In file included from LL_funcs.c:1:0:
 common.h:22:1: error: unknown type name Agdict_t
LL_funcs.c:531:13: error: too few arguments to function agedge
/usr/local/include/graphviz/cgraph.h:286:18: note: declared here
make: *** [LL_funcs.o] Error 1
ERROR: compilation failed for package Rgraphviz
* removing â/home/fpkerckh/R/x86_64-pc-linux-gnu-library/3.1/Rgraphvizâ

Does anybody have some pointers here? I have been trying a lot of things, including compiling from source and using github package versions and so on so I would be very happy if somebody can help me out.

 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] devtools_1.5         BiocInstaller_1.14.2

loaded via a namespace (and not attached):
[1] digest_0.6.4   evaluate_0.5.3 httr_0.3       memoise_0.2.1  parallel_3.1.0
[6] RCurl_1.95-4.1 stringr_0.6.2  tools_3.1.0    whisker_0.3-2

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