[BioC] Problems building RBGL package

[Rasmus Ory Nielsen]

Hi,

I am not able to build the RBGL package (needed for the GOstats package). See 
build output below.

My system is running Fedora 9 x86_64 with all upgrades.
R-2.7.0-5.fc9.x86_64
gcc-4.3.0-8.x86_64
gcc-c++-4.3.0-8.x86_64

Thanks in advance.

Best regards,
Rasmus Ory Nielsen


 > biocLite(c("RBGL"))
Running biocinstall version 2.2.9 with R version 2.7.0
Your version of R requires version 2.2 of BioConductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
   argument 'lib' is missing: using '/usr/lib64/R/library'
trying URL 
'http://bioconductor.org/packages/2.2/bioc/src/contrib/RBGL_1.16.0.tar.gz'
Content type 'application/x-gzip' length 1327240 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -m64 -I/usr/include/R  -I/usr/local/include   -IboostIncl  -fpic  -O2 -g 
-pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m64 -mtune=generic -c bbc.cpp -o bbc.o
In file included from 
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../include/c++/4.3.0/ext/hash_set:64,
                  from boostIncl/boost/graph/adjacency_list.hpp:22,
                  from RBGL.hpp:26,
                  from bbc.cpp:1:
/usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../include/c++/4.3.0/backward/backward_warning.h:32:2: 
warning: #warning This file includes at least one deprecated or antiquated 
header which may be removed without further notice at a future date. Please 
use a non-deprecated interface with equivalent functionality instead. For a 
listing of replacement headers and interfaces, consult the file 
backward_warning.h. To disable this warning use -Wno-deprecated.
In file included from boostIncl/boost/graph/dijkstra_shortest_paths.hpp:19,
                  from boostIncl/boost/graph/betweenness_centrality.hpp:14,
                  from bbc.cpp:2:
boostIncl/boost/pending/relaxed_heap.hpp: In member function 'size_t 
boost::relaxed_heap<IndexedType, Compare, ID>::log_base_2(size_t)':
boostIncl/boost/pending/relaxed_heap.hpp:101: error: 'CHAR_BIT' was not 
declared in this scope
make: *** [bbc.o] Error 1
chmod: cannot access `/usr/lib64/R/library/RBGL/libs/*': No such file or directory
ERROR: compilation failed for package 'RBGL'
** Removing '/usr/lib64/R/library/RBGL'