Opened 12 years ago

Closed 12 years ago

#38204 closed defect (fixed)

arb @5.5: Disable compiler optimization to fix runtime crash of fast aligner

Reported by: mattcottrell Owned by: larryv (Lawrence Velázquez)
Priority: Normal Milestone:
Component: ports Version:
Keywords: maintainer haspatch Cc:
Port: arb

Description

Users of the arb port have reported a runtime crash in the DNA sequence fast aligner. The attached patches work around that crash by reducing the level of compiler optimization from -O4 to -O0. The upstream developers are aware of the problem and are working on a long term solution that will appear in their next arb release. The attached patches make it possible for all arb 5.5 users to get their work done using MacPorts.

Attachments (2)

Portfile.diff (793 bytes) - added by mattcottrell 12 years ago.
Portfile diff reduces compiler optimization
patch-ARB-Makefile.diff (317 bytes) - added by mattcottrell 12 years ago.
Makefile now specifies -O0 compiler optimization

Download all attachments as: .zip

Change History (6)

Changed 12 years ago by mattcottrell

Attachment: Portfile.diff added

Portfile diff reduces compiler optimization

Changed 12 years ago by mattcottrell

Attachment: patch-ARB-Makefile.diff added

Makefile now specifies -O0 compiler optimization

comment:1 Changed 12 years ago by larryv (Lawrence Velázquez)

Owner: changed from macports-tickets@… to larryv@…
Status: newassigned
Summary: Reduce compiler optimization to fix arb runtime crash of fast alignerarb @5.5: Disable compiler optimization to fix runtime crash of fast aligner
Version: 2.1.3

Thanks.

comment:2 Changed 12 years ago by larryv (Lawrence Velázquez)

The arb port already contains a file named patch-ARB-makefile.diff, but it doesn’t seem to be used. Would it be okay if I overwrote that one?

comment:3 in reply to:  2 Changed 12 years ago by mattcottrell

Replying to larryv@…:

The arb port already contains a file named patch-ARB-makefile.diff, but it doesn’t seem to be used. Would it be okay if I overwrote that one?

Yes, please use the new Makefile patch.

Thanks - Matt

comment:4 Changed 12 years ago by larryv (Lawrence Velázquez)

Resolution: fixed
Status: assignedclosed

Committed in r103435. Thanks!

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