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

[Charles Plessy]

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