Re: [Seqan-dev] SeqAn with valgrind

[John Reid <j.reid@mail.cryst.bbk.ac.uk>]

Dear Dave,

It is probably something I'm doing then. I'll have a look. Thanks for the suppression file.

John.

On 07/06/13 08:08, Weese, David wrote:

Hi John,

we use valgrind in our nightly builds with gcc-4.6 under Linux without any issues and so far haven't seen that error. Do you get the same error with our tests, e.g. test_index_stree_iterators or test_index_repeats?

If not could you please create a bug ticket with some sources how to reproduce the error?

Thanks,
Dave

PS: This is our valgrind suppression file:

--
David Weese                     weese@inf.fu-berlin.de
Freie Universität Berlin        http://www.inf.fu-berlin.de/
Institut für Informatik         Phone: +49 30 838 75137
Takustraße 9                    Algorithmic Bioinformatics
14195 Berlin                    Room 020

Am 06.06.2013 um 15:31 schrieb John Reid <j.reid@mail.cryst.bbk.ac.uk>:

> Hi all,
>
> Is valgrind a tool that people use with SeqAn much? Is SeqAn free of any
> spurious (or not so spurious) leaks? Does anyone have a valgrind
> suppressions file I might find useful with gcc-4.6? For instance I have
> the following reported by "valgrind --leak-check=full" when using a
> TopDown iterator with an ESA. I'm guessing it is not a problem but I'd
> like to see what others think. Getting rid of any valgrind warnings
> generated by SeqAn will help me locate any bugs I might have in my code.
>
> Thanks again for a fantastic library,
> John.
>
> ==16613== Memcheck, a memory error detector
> ==16613== Copyright (C) 2002-2011, and GNU GPL'd, by Julian Seward et al.
> ==16613== Using Valgrind-3.7.0 and LibVEX; rerun with -h for copyright info
> ==16613== Command: /usr/bin/python /usr/bin/nosetests ../cacto/
> ==16613==
> ..==16613== Conditional jump or move depends on uninitialised value(s)
> ==16613==    at 0x9FD1E6F: void
> seqan::createChildtab<seqan::String<unsigned long, seqan::Alloc<void> >,
> seqan::String<unsigned long, seqan::Alloc<void> >
>> (seqan::String<unsigned long, seqan::Alloc<void> >&, seq
> an::String<unsigned long, seqan::Alloc<void> > const&)
> (index_childtab.h:261)
> ==16613==    by 0x9FC6278: bool
> seqan::indexCreate<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexEsa
> <void>
>> (seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexEsa<void> >&,
> seqan::Tag<seqan::
> FibreChildtab_>, seqan::Childtab) (index_shims.h:608)
> ==16613==    by 0x9FB9373: bool
> seqan::indexCreate<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexEsa
> <void>,
> seqan::FibreChildtab_>(seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexEsa<void>
>> &, seqan::Tag<seqan::FibreChildtab_>) (index_shims.h:615)
> ==16613==    by 0x9FACCA2: bool
> seqan::indexRequire<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexEs
> a<void>,
> seqan::FibreChildtab_>(seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexEsa<void>
>> &, seqan::Tag<seqan::FibreChildtab_>) (index_shims.h:664)
> ==16613==    by 0x9FA0B93: void
> seqan::_indexRequireTopDownIteration<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> >
>> ,
> void>(seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexEsa<void> >&)
> (index_esa_base.h:
> 303)
> ==16613==    by 0x9F966DA:
> seqan::Iter<seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >,
> seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexEs
> a<void> >, seqan::VSTree<seqan::TopDown<seqan::Preorder> >
>> ::Iter(seqan::Index<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned
> char, seqan::Dna_>, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::D
> efault_> > >, seqan::IndexEsa<void> >&) (index_esa_stree.h:133)
>
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