Mark Kimpel
2008-Jun-27 16:14 UTC
[Rd] RBGL not compiling on Debian Lenny with c++ (Debian 4.3.1-2) 4.3.1
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)
Kasper Daniel Hansen
2008-Jun-27 16:42 UTC
[Rd] RBGL not compiling on Debian Lenny with c++ (Debian 4.3.1-2) 4.3.1
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) > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel