[BioC] Problems building RBGL package
Rasmus Ory Nielsen
rasmus.nielsen at agrsci.dk
Wed Jun 25 10:03:20 CEST 2008
Hi,
Here's the patch.
RBGL_1.16.0-fixheader.patch:
diff -up RBGL/RBGL/src/boostIncl/boost/pending/relaxed_heap.hpp.fixheader
RBGL/RBGL/src/boostIncl/boost/pending/relaxed_heap.hpp
--- RBGL/RBGL/src/boostIncl/boost/pending/relaxed_heap.hpp.fixheader
2008-06-24 15:22:57.000000000 +0200
+++ RBGL/RBGL/src/boostIncl/boost/pending/relaxed_heap.hpp 2008-06-24
15:23:06.000000000 +0200
@@ -13,6 +13,7 @@
#include <boost/property_map.hpp>
#include <boost/optional.hpp>
#include <vector>
+#include <climits>
#ifdef BOOST_RELAXED_HEAP_DEBUG
# include <iostream>
Best regards,
Rasmus Ory Nielsen
Rasmus Ory Nielsen skrev:
> 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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>>>
>>
>
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