[BioC] Problems building RBGL package

[Rasmus Ory Nielsen]

Hi Li,

Thank you for your quick answer.

I think the problem is GCC 4.3 is more strict about headers, see [1] and [2].
I got RGBL to compile by including <climits> in 
boostIncl/boost/pending/relaxed_heap.hpp.

[1] http://gcc.gnu.org/gcc-4.3/porting_to.html
[2] http://mail-archive.com/pld-cvs-commit@lists.pld-linux.org/msg140605.html

Thanks.

Best regards,
Rasmus Ory Nielsen


Li Long skrev:
> Since CHAR_BIT is set in /usr/include/limits.h (or similar include path
> from the system), you should also check to make sure your gcc looks into
> those dirs as well.
> 
> 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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>