Hi Mark
This issue (I think) was recently discussed on the BioC list. The
upshot of that conversation was that Boost (not RBGL) has a problem
with GCC 4.3. You'll need to fix the headers of boost which is rather
simple, there is a fix in the Bioconductor thread.
Kasper
On Jun 27, 2008, at 9:14 AM, Mark Kimpel wrote:
I've just installed Debian Lenny and RBGL fails compilation with the
following errors (sessionInfo() follows).
* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include
-I/usr/local/include -IboostIncl -fpic -g -O2 -c bbc.cpp -o bbc.o
In file included from /usr/include/c++/4.3/ext/hash_set:64,
from boostIncl/boost/graph/adjacency_list.hpp:22,
from RBGL.hpp:26,
from bbc.cpp:1:
/usr/include/c++/4.3/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
sessionInfo()
R version 2.7.1 Patched (2008-06-26 r45997)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE
=
en_US
.UTF
-8
;LC_NUMERIC
=
C
;LC_TIME
=
en_US
.UTF
-8
;LC_COLLATE
=
en_US
.UTF
-8
;LC_MONETARY
=
C
;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:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] graph_1.18.1
loaded via a namespace (and not attached):
[1] cluster_1.11.11 tcltk_2.7.1 tools_2.7.1
--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
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