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

Mon May 14 09:09:36 UTC 2012

Hi Alex,

I would go for a push to 2.0, great you spotted that.

Cheers,

Steffen

-------- Original-Nachricht --------
> Datum: Mon, 14 May 2012 09:32:29 +0200
> Von: Alex Mestiashvili <alex at biotec.tu-dresden.de>
> An: debian-med-packaging at lists.alioth.debian.org
> Betreff: Re: [Debian-med-packaging] Bug#672744: Bug#672744: cufflinks: needs rebuild against boost 1.49

> 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
> >>
> >>
> >>
> >> _______________________________________________
> >> Debian-med-packaging mailing list
> >> Debian-med-packaging at lists.alioth.debian.org
> >>
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> >>
> >>     
> 
> 
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