Question: RGraphiz installation keeps on failing ubuntu 12.04 LTS server
5.5 years ago by
Guest User • 12k
Guest User • 12k 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 ??/home/fpkerckh/R/x86_64-pc-linux-gnu- library/3.1/Rgraphviz?? 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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  devtools_1.5 BiocInstaller_1.14.2 loaded via a namespace (and not attached):  digest_0.6.4 evaluate_0.5.3 httr_0.3 memoise_0.2.1 parallel_3.1.0  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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