[BioC] Problems building RBGL package

[Rasmus Ory Nielsen]

Hi Li,

Any hope for an updated version of the RBGL package?

Best regards,
Rasmus Ory Nielsen


Rasmus Ory Nielsen skrev:
> 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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>>
> 
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