[Bug 1291021] New: Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
Bug ID: 1291021 Summary: Review Request: debruijn - Software for the generation de Bruijn sequences for neuroscience experiments Product: Fedora Version: rawhide Component: Package Review Severity: medium Priority: medium Assignee: nobody@fedoraproject.org Reporter: i.gnatenko.brain@gmail.com QA Contact: extras-qa@fedoraproject.org CC: package-review@lists.fedoraproject.org
Spec URL: https://ignatenkobrain.fedorapeople.org/neurofedora/debruijn.spec SRPM URL: https://ignatenkobrain.fedorapeople.org/neurofedora/debruijn-0.0.0-0.1.git15... Description: Software for the generation de Bruijn sequences for neuroscience experiments. Fedora Account System Username: ignatenkobrain
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
Igor Gnatenko i.gnatenko.brain@gmail.com 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
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED CC| |zbyszek@in.waw.pl Assignee|nobody@fedoraproject.org |zbyszek@in.waw.pl Flags| |fedora-review?
--- Comment #1 from Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl --- - 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.
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
--- Comment #2 from Igor Gnatenko i.gnatenko.brain@gmail.com --- Fixed. Links are the same.
I tried to figure out what happened with this program, but I cant fix crashing =(
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
--- Comment #3 from Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl --- 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.
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
--- Comment #4 from Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl --- (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.
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
--- Comment #5 from Zbigniew Jędrzejewski-Szmek zbyszek@in.waw.pl --- ?
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |sanjay.ankur@gmail.com Flags| |needinfo?(i.gnatenko.brain@ | |gmail.com)
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
Igor Gnatenko i.gnatenko.brain@gmail.com 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 i.gnatenko.brain@gmail.com --- Unfortunately I don't have time to work on these review requests anymore, sorry.
https://bugzilla.redhat.com/show_bug.cgi?id=1291021
Ankur Sinha (FranciscoD) sanjay.ankur@gmail.com 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.
package-review@lists.fedoraproject.org
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