RBGL not compiling on Debian Lenny with c++ (Debian 4.3.1-2) 4.3.1

[Mark Kimpel]

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

[phone] Work, & Mobile & VoiceMail
[phone] Home (no voice mail please)

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[Kasper Daniel Hansen]

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
>
> [phone] Work, & Mobile & VoiceMail
> [phone] Home (no voice mail please)
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

______________________________________________
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https://stat.ethz.ch/mailman/listinfo/r-devel