Some time ago I had difficulty installing RBGL with Ubuntu Hardy on R-2.7.0
and the problem was attributed to an with BGL. I got some very helpful
advice and posted a script to fix the problem by hacking the RGBL source
code:
dateTue, Jan 15, 2008 at 2:16 PMsubjectRe: [R-sig-Debian] trouble installing
building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64mailing
listr-sig-debian.r-project.org The problem is now also occurring since I
switched to Debian Lenny and R-2.6.8 (devel) [see output below]. My first
step would be to download the development version of RGBL but I can't for
the life of me find where to download tarballs of development packages from
CRAN (BioConductor makes this very straightforward for its packages BTW).

So, are other people using bleeding-edge installations having this issue? Is
a fix on the horizon? If it's not within a few months a lot of standard
installations will break. Finally, does anyone know where to find the
development version tarballs of packages (probably a better ? for R-devel
but I"m trying to avoid multiple postings).

Thanks, Mark

* Installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
g++ -I/home/mkimpel/R_HOME/R-devel/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
chmod: cannot access `/home/mkimpel/R_HOME/site-library-2.8.0/RBGL/libs/*':
No such file or directory
ERROR: compilation failed for package 'RBGL'
** Removing '/home/mkimpel/R_HOME/site-library-2.8.0/RBGL'
** Restoring previous '/home/mkimpel/R_HOME/site-library-2.8.0/RBGL'

The downloaded packages are in
    /tmp/RtmpKH9g98/downloaded_packages
Warning message:
In install.packages("RBGL") :
  installation of package 'RBGL' had non-zero exit status
>

-- 
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)

******************************************************************

	[[alternative HTML version deleted]]

