[Bug 1291021] Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1291021

Ankur Sinha (FranciscoD)  changed:

   What|Removed |Added

 Blocks||201449 (FE-DEADREVIEW)




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=201449
[Bug 201449] FE-DEADREVIEW -- Reviews stalled due to lack of submitter
response should be blocking this bug.
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[Bug 1291021] Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1291021

Igor Gnatenko  changed:

   What|Removed |Added

 Status|ASSIGNED|CLOSED
 Resolution|--- |WONTFIX
  Flags|needinfo?(i.gnatenko.brain@ |
   |gmail.com)  |
Last Closed||2018-08-22 03:31:21



--- Comment #6 from Igor Gnatenko  ---
Unfortunately I don't have time to work on these review requests anymore,
sorry.

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[Bug 1291021] Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1291021

Ankur Sinha (FranciscoD)  changed:

   What|Removed |Added

 CC||sanjay.an...@gmail.com
  Flags||needinfo?(i.gnatenko.brain@
   ||gmail.com)



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[Bug 1291021] Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1291021



--- Comment #5 from Zbigniew Jędrzejewski-Szmek  ---
?

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[Bug 1291021] Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1291021



--- Comment #4 from Zbigniew Jędrzejewski-Szmek  ---
(In reply to Zbigniew Jędrzejewski-Szmek from comment #3)
> It seems that it makes very large allocations on the stack. But even if
> those are changed to use the heap, function calls recurse very deeply and
> fill the stack. So there's no obvious "error", just the program is designed
> in a way where it cannot be used with large arguments.
In case the intent wasn't clear: I'm trying to say this crashiness is ugly, but
not something to hold up the review.

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[Bug 1291021] Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1291021



--- Comment #3 from Zbigniew Jędrzejewski-Szmek  ---
chmod -x ... build ..., and then pushd build fails with permission denied :(

%check is missing the name of the program to run...

Why do you need cmake? Isn't the upstream Makefile good enough?

It seems that it makes very large allocations on the stack. But even if those
are changed to use the heap, function calls recurse very deeply and fill the
stack. So there's no obvious "error", just the program is designed in a way
where it cannot be used with large arguments.

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[Bug 1291021] Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1291021



--- Comment #2 from Igor Gnatenko  ---
Fixed. Links are the same.

I tried to figure out what happened with this program, but I cant fix crashing
=(

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[Bug 1291021] Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1291021

Zbigniew Jędrzejewski-Szmek  changed:

   What|Removed |Added

 Status|NEW |ASSIGNED
 CC||zbys...@in.waw.pl
   Assignee|nob...@fedoraproject.org|zbys...@in.waw.pl
  Flags||fedora-review?



--- Comment #1 from Zbigniew Jędrzejewski-Szmek  ---
- software is under an acceptable license (BSD with adv.)
- latest (git) snapshot
- license file is wrong, but upstream has been notified
- no scriptlets
- requires/provides are OK
- new python packaging template is used
- builds and installs OK
- fedora-review is happy

You can drop '%doc README.md', the README is essentially empty.

There's a compiled binary repo in the archive, remove it in %prep to be sure
it's not packaged by mistake.

Add %check:
%{buildroot}%{_bindir}/debruijn 12 3

It seems fairly easy to crash it by specifying sufficiently large values:
$ debruijn 12 8
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted (core dumped)

valgrind in general is not too happy with the binary ;)

rpmlint:
debruijn.i686: W: spelling-error Summary(en_US) de -> DE, ed, d
debruijn.i686: W: spelling-error Summary(en_US) neuroscience -> pseudoscience
debruijn.i686: W: spelling-error %description -l en_US de -> DE, ed, d
debruijn.i686: W: spelling-error %description -l en_US neuroscience ->
pseudoscience
rpmlint is prescient!

debruijn.i686: W: no-manual-page-for-binary debruijn
debruijn.src: W: spelling-error Summary(en_US) de -> DE, ed, d
debruijn.src: W: spelling-error Summary(en_US) neuroscience -> pseudoscience
debruijn.src: W: spelling-error %description -l en_US de -> DE, ed, d
debruijn.src: W: spelling-error %description -l en_US neuroscience ->
pseudoscience
debruijn-debuginfo.i686: W: spurious-executable-perm
/usr/src/debug/DeBruijn-1563f6f8833d88b7cde399cbf93f35b8b4b81586/debruijn.cpp
debruijn-debuginfo.i686: W: spurious-executable-perm
/usr/src/debug/DeBruijn-1563f6f8833d88b7cde399cbf93f35b8b4b81586/debruijn.h
3 packages and 0 specfiles checked; 0 errors, 11 warnings.

All OK.

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[Bug 1291021] Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments

[bugzilla]

https://bugzilla.redhat.com/show_bug.cgi?id=1291021

Igor Gnatenko  changed:

   What|Removed |Added

 Blocks||1276941 (fedora-neuro)
  Alias||debruijn




Referenced Bugs:

https://bugzilla.redhat.com/show_bug.cgi?id=1276941
[Bug 1276941] Fedora NeuroImaging and NeuroScience tracking bug
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