From khansen at stat.Berkeley.EDU  Fri Jun 27 18:42:12 2008
From: khansen at stat.Berkeley.EDU (Kasper Daniel Hansen)
Date: Fri, 27 Jun 2008 09:42:12 -0700
Subject: [Rd] RBGL not compiling on Debian Lenny with c++ (Debian
	4.3.1-2) 4.3.1
In-Reply-To: <6b93d1830806270914l36321e58na5f749d40f699eaf@mail.gmail.com>
References: <6b93d1830806270914l36321e58na5f749d40f699eaf@mail.gmail.com>
Message-ID: <748FD7C5-B405-4D33-BC61-DA38FCEBF02A@stat.berkeley.edu>

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



[Rd] RBGL not compiling on Debian Lenny with c++ (Debian 4.3.1-2) 4.3.1
Kasper Daniel Hansen