[BioC] Problems building RBGL package

[Rasmus Ory Nielsen]

Hi Li,

OK, I see.

In case other people experiences the same problem, I have attached a short 
patch showing the fix I made. I don't know if it is "The Right Way" to do it, 
but it works for me.

Best regards,
Rasmus Ory Nielsen


Li Long skrev:
> It seems the issue is compiler related.
> 
> Gcc 4.3.1 is released earlier this month, after 4.3.0 in Mar, which is
> pretty new.  We don't have enough man-power to lock-step with each and
> every compiler release.
> 
> Boost's new release complies with 4.2.1.   Since the boost part is taken
> directly from release, it's not so hot idea (from my point of view) to
> manually tweek it individually.  Probably we'll wait for the part that's
> compiler-related.  I might do something to put in the newer functions from
> Graph sometime in the summer.
> 
> Even if we have new codes, it wouldn't be in release until Oct.
> 
> Li
> 
> 
> 
>> 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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>>
>