[BioC] Problems building RBGL package

[Li Long]

I suggest double-check the options you used:

> -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic

by default, we don't set any of these for RBGL.  I suspect they alter the
options when expanding templates, and lead to

> error: 'CHAR_BIT' was not declared in this scope

which is from boost.

Li



> Hi,
>
> I am not able to build the RBGL package (needed for the GOstats package).
> See
> build output below.
>
> My system is running Fedora 9 x86_64 with all upgrades.
> R-2.7.0-5.fc9.x86_64
> gcc-4.3.0-8.x86_64
> gcc-c++-4.3.0-8.x86_64
>
> Thanks in advance.
>
> Best regards,
> Rasmus Ory Nielsen
>
>
>  > biocLite(c("RBGL"))
> Running biocinstall version 2.2.9 with R version 2.7.0
> Your version of R requires version 2.2 of BioConductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  :
>    argument 'lib' is missing: using '/usr/lib64/R/library'
> trying URL
> 'http://bioconductor.org/packages/2.2/bioc/src/contrib/RBGL_1.16.0.tar.gz'
> Content type 'application/x-gzip' length 1327240 bytes (1.3 Mb)
> opened URL
> ==================================================
> downloaded 1.3 Mb
>
> * Installing *source* package 'RBGL' ...
> untarring boost include tree...
> ** libs
> g++ -m64 -I/usr/include/R  -I/usr/local/include   -IboostIncl  -fpic  -O2
> -g
> -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c bbc.cpp -o bbc.o
> In file included from
> /usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../include/c++/4.3.0/ext/hash_set:64,
>                   from boostIncl/boost/graph/adjacency_list.hpp:22,
>                   from RBGL.hpp:26,
>                   from bbc.cpp:1:
> /usr/lib/gcc/x86_64-redhat-linux/4.3.0/../../../../include/c++/4.3.0/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 `/usr/lib64/R/library/RBGL/libs/*': No such file or
> directory
> ERROR: compilation failed for package 'RBGL'
> ** Removing '/usr/lib64/R/library/RBGL'
>
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