You are trying two things
1) Install very latest Rgraphviz from github
2) Install Rgraphviz using an external Graphviz, which is what you show the
output of.

2) is likely to fail given how new a Graphviz you're using.  I would like
to see full output of 1).

Best,
Kasper


On Mon, Apr 28, 2014 at 2:09 PM, Frederiek - Maarten Kerckhof [guest] <
guest@bioconductor.org> wrote:

>
> Hi,
>
> 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 Ã¢/home/fpkerckh/R/x86_64-pc-linux-gnu-library/3.1/RgraphvizÃ¢
>
> 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)
>
> 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] 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
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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