[Debian-med-packaging] Bug#672744: Bug#672744: cufflinks: needs rebuild against boost 1.49

[Alex Mestiashvili]

Hello,
FYI
The new upstream version 2.0.0 is available.
But it still fails to build. I think it makes sense to patch the new one.
Should I push the new one or should I wait with it ?
Best regards,
Alex

On 05/14/2012 08:58 AM, Andreas Tille wrote:
> Hi,
>
> please inspect the patch provided here:
>
>    http://anonscm.debian.org/gitweb/?p=debian-med/cufflinks.git;a=blob;f=debian/patches/gcc-4.7.patch;h=63bfaede309d5a549f59a86f991a12297d993abf;hb=HEAD
>
> It fixes the build issue but I'm not fully sure whether it is what the
> code is supposed to be.
>
> Kind regards
>
>        Andreas.
>
> On Mon, May 14, 2012 at 08:03:30AM +0900, Charles Plessy wrote:
>   
>> Dear Cufflinks developers,
>>
>> we are distributing Cufflinks (and Bowtie, and Tophat) in Debian.  Recently we
>> changed our default compiler to be GCC 4.7, and unfortunately Cufflinks does
>> not build with it.  I have committed and pushed the build log at the following
>> URL.
>>
>> http://git.debian.org/?p=debian-med/cufflinks.git;a=blob;f=log;h=82d67ddf64cf1c0db584763c474dbfce2ff39f82;hb=cbcfb480416b4ac4e6fc45b0b2c53dc64433a002
>>
>> The relevant part is:
>>
>> assemble.cpp: In function 'void create_reachability_bp_graph(DAG&, ReachGraph&, std::vector<lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::BNode, std::allocator<lemon::BidirBpUGraphExtender<lemon::SmartBpUGraphBase>::BNode> >, DagToBp&, const boost::adjacency_list<>&, const std::vector<bool>&)':
>> assemble.cpp:123:17: warning: variable 'hits_for_node' set but not used [-Wunused-but-set-variable]
>> In file included from ./lemon/list_graph.h:26:0,
>>                  from ./lemon/dfs.h:26,
>>                  from ./lemon/topology.h:22,
>>                  from assemble.cpp:19:
>> ./lemon/bits/base_extender.h: In instantiation of 'lemon::BidirBpUGraphExtender<Base>::Node lemon::BidirBpUGraphExtender<Base>::source(const UEdge&) const [with Base = lemon::SmartBpUGraphBase; lemon::BidirBpUGraphExtender<Base>::Node = lemon::SmartBpUGraphBase::Node; lemon::BidirBpUGraphExtender<Base>::UEdge = lemon::SmartBpUGraphBase::UEdge]':
>> assemble.cpp:258:36:   required from here
>> ./lemon/bits/base_extender.h:362:21: error: 'aNode' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
>> ./lemon/bits/base_extender.h:362:21: note: declarations in dependent base 'lemon::SmartBpUGraphBase' are not found by unqualified lookup
>> ./lemon/bits/base_extender.h:362:21: note: use 'this->aNode' instead
>> ./lemon/bits/base_extender.h: In instantiation of 'lemon::BidirBpUGraphExtender<Base>::Node lemon::BidirBpUGraphExtender<Base>::target(const UEdge&) const [with Base = lemon::SmartBpUGraphBase; lemon::BidirBpUGraphExtender<Base>::Node = lemon::SmartBpUGraphBase::Node; lemon::BidirBpUGraphExtender<Base>::UEdge = lemon::SmartBpUGraphBase::UEdge]':
>> assemble.cpp:259:36:   required from here
>> ./lemon/bits/base_extender.h:365:21: error: 'bNode' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
>> ./lemon/bits/base_extender.h:365:21: note: declarations in dependent base 'lemon::SmartBpUGraphBase' are not found by unqualified lookup
>> ./lemon/bits/base_extender.h:365:21: note: use 'this->bNode' instead
>> make[3]: *** [assemble.o] Error 1
>>
>> I looked in the Lemon library's website so see if there was a correction
>> available, but it looks that in the latest version, ./lemon/bits/base_extender.h
>> does not exist anymore.
>>
>> Please do not hesitate to contact us in case you would like us to test
>> patches before releasing an update.
>>
>> By the way, we are already applying three patches to Cufflinks.
>>
>>   http://anonscm.debian.org/gitweb/?p=debian-med/cufflinks.git;a=tree;f=debian/patches;h=181a8624688d76a6c0a7257e96f3ba80671e7169;hb=HEAD
>>
>> The first fixes some spelling, the second and the third normalise the path to
>> the samtools headers to the one we chose for Debian (other programs, like the
>> BioPerl Bio::Samtools library, were following other paths).
>>
>> Ubuntu also patches Cufflinks, so that it can be built on 32-bit systems.
>>
>>   http://patches.ubuntu.com/c/cufflinks/cufflinks_1.3.0-1ubuntu2.patch 
>>
>> Have a nice day,
>>
>> -- 
>> Charles Plessy
>> Debian Med packaging team,
>> http://www.debian.org/devel/debian-med
>> Tsurumi, Kanagawa, Japan
>>
>>
>>
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>>
>>