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Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails)

From	Nilesh Patra <nilesh@iki.fi>
Newsgroups	linux.debian.bugs.dist
Subject	Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails)
Date	2024-12-08 11:10 +0100
Message-ID	<JRmoF-eFNq-3@gated-at.bofh.it> (permalink)
References	(4 earlier) <JR0Hw-ep89-5@gated-at.bofh.it> <JR3m1-eqN4-3@gated-at.bofh.it> <JRliV-eEqG-1@gated-at.bofh.it> <Ikbw0-u9x-127@gated-at.bofh.it> <JRliV-eEqG-1@gated-at.bofh.it>
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On 08/12/24 14:23, Nilesh Patra wrote:
> 
> 
> On 07/12/24 18:53, Nilesh Patra wrote:
>> On 07/12/24 4:25 pm, Étienne Mollier wrote:
>>> There does not seem to have been much changes.  Maybe the error
>>> is somewhere else?  I hope I ran the test properly, it was a bit
>>> intricate.
>>
>> Your earlier reply to the bug report had this trace:
>>
>> /usr/include/c++/14/bits/stl_vector.h:1130:
>>          std::vector<_Tp, _Alloc>::reference
>>          std::vector<_Tp, _Alloc>::operator[](size_type)
>>          [
>>              with _Tp = ChainedMatchPos;
>>              _Alloc = std::allocator<ChainedMatchPos>;
>>              reference = ChainedMatchPos&;
>>              size_type = long unsigned int
>>          ]: Assertion '__n < this->size()' failed.
>>      /tmp/autopkgtest.WdOt0L/build.sPS/src/debian/tests/run-unit-
>>
>> The Assertion failure "'__n < this->size()' failed." indicates that the index is going out of bounds in the vector. (upper bound)
>>
>> Do you still see this trace? If so, maybe the versions are not tested correctly?ensuring blasr is built against patches pbseqlib?
> 
> I tried this on a debian:unstable docker container and it does seem to pass for me
> 

Now, I tried it on salsa CI as well with creating aptly of updated pbseqlib and modifying blasr's salsa
CI yml on a diff branch to consume it, see: https://salsa.debian.org/med-team/blasr/-/commit/502cd60ec57ec2eb953abb9a308600201f3df3f1

As expected updated pbseqlib which gets
pulled in blasr's salsa CI (https://salsa.debian.org/med-team/blasr/-/jobs/6719902#L656)

This is the result on plain build: https://salsa.debian.org/med-team/blasr/-/jobs/6719809
With patched pbseqlib: https://salsa.debian.org/med-team/blasr/-/jobs/6719964

I do not have my yubikey handy right now. Do you think you can sponsor pbseqlib if all looks good here?

I will delete these branches (fiddle-salsa) on both repos when I have time.

-n

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Bug#1067374: blasr: FTBFS fixed by itself (but autopkgtest fails) Nilesh Patra <nilesh@iki.fi> - 2024-12-08 11:10 +0100

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