[BioC] RBGL 1.2.2 compilation problem

[Roels, Steven]

Hello all,

I'm using R 1.9.1 Patched (2004-09-07) plus Bioconductor 1.4 on a
solaris8/sun4u system building with gcc 3.4.0 and I'm having problems
with the release version (1.2.2) of RBGL. (I've been able to get all
other packages loaded).

First is the previously reported issue with the z option of tar, but
even with that fixed, I get the errors below.

Versions 1.2.5 and the latest 1.3.7 work (or at least install fine), but
as has been pointed out many times, one should not use devel versions of
Bioconductor modules with non-devel versions of R.  So, is use of one or
the other devel version OK here?  If not, is there a quick patch to the
1.4 release that could be done, or a workaround for 1.2.2?

Thanks,

-Steve

kobuk% /prod/ddm/tools/R/R-1.9.1_Bioconductor-1.4/bin/R CMD INSTALL RBGL

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/prod/ddm/tools/R/R-1.9.1_Bioconductor-1.4/lib/R/include
-I/prod/ddm/usr/local/include -I/prod/ddm/usr/local/include/glib-2.0
 -I/prod/ddm/usr/local/lib/glib-2.0/include -I/mpi/solaris8/usr/include
-I/mpi/usr/include -I/usr/local/include  -IboostIncl -ftempl
ate-depth-30 -g -fPIC  -g -O2 -c interfaces.cpp -o interfaces.o
In file included from boostIncl/boost/config.hpp:35,
                 from RBGL.h:4,
                 from interfaces.cpp:1:
boostIncl/boost/config/compiler/gcc.hpp:66:7: warning: #warning "Unknown
compiler version - please run the configure tests and repor
t the results"
In file included from boostIncl/boost/graph/adjacency_list.hpp:48,
                 from RBGL.h:13,
                 from interfaces.cpp:1:
boostIncl/boost/graph/detail/edge.hpp:99: error: `std::ostream' is not a
template
boostIncl/boost/graph/detail/edge.hpp:100: error: `std::ostream' is not
a template
In file included from
boostIncl/boost/graph/dijkstra_shortest_paths.hpp:39,
                 from RBGL.h:16,
                 from interfaces.cpp:1:
boostIncl/boost/pending/mutable_queue.hpp: In member function `bool
boost::mutable_queue<IndexedType, RandomAccessContainer, Comp, I
D>::test()':
boostIncl/boost/pending/mutable_queue.hpp:131: error: `is_heap' is not a
member of `std'
In file included from RBGL.h:24,
                 from interfaces.cpp:1:
boostIncl/boost/graph/strong_components.hpp: In function `typename
boost::property_traits<ColorMap>::value_type boost::kosaraju_stro
ng_components(Graph&, ComponentsMap, FinishTime, ColorMap)':
boostIncl/boost/graph/strong_components.hpp:333: error: `f' undeclared
(first use this function)
boostIncl/boost/graph/strong_components.hpp:333: error: (Each undeclared
identifier is reported only once for each function it appea
rs in.)
make: *** [interfaces.o] Error 1
ERROR: compilation failed for package 'RBGL'
** Removing
'/prod/ddm/tools/R/R-1.9.1_Bioconductor-1.4/lib/R/library/RBGL'



*****************************************************************
Steve Roels, Ph.D.                       
Senior Scientist I
Computational Biology     
Millennium Pharmaceuticals, Inc.   Phone: 617.761.6820
640 Memorial Drive                 FAX:   617.577.3555
Cambridge, MA 02139-4815           Email: steven.roels at mpi.com
*****************************************************************




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