[MacPorts] #38204: Reduce compiler optimization to fix arb runtime crash of fast aligner
#38204: Reduce compiler optimization to fix arb runtime crash of fast aligner ---------------------------------+-------------------------------- Reporter: matt.cottrell@… | Owner: macports-tickets@… Type: defect | Status: new Priority: Normal | Milestone: Component: ports | Version: 2.1.3 Keywords: maintainer haspatch | Port: arb ---------------------------------+-------------------------------- 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. -- Ticket URL: <https://trac.macports.org/ticket/38204> MacPorts <http://www.macports.org/> Ports system for Mac OS
#38204: arb @5.5: Disable compiler optimization to fix runtime crash of fast aligner ------------------------------+--------------------------------- Reporter: matt.cottrell@… | Owner: larryv@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: maintainer haspatch Port: arb | ------------------------------+--------------------------------- Changes (by larryv@…): * status: new => assigned * owner: macports-tickets@… => larryv@… * version: 2.1.3 => Comment: Thanks. -- Ticket URL: <https://trac.macports.org/ticket/38204#comment:1> MacPorts <http://www.macports.org/> Ports system for Mac OS
#38204: arb @5.5: Disable compiler optimization to fix runtime crash of fast aligner ------------------------------+--------------------------------- Reporter: matt.cottrell@… | Owner: larryv@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: maintainer haspatch Port: arb | ------------------------------+--------------------------------- Comment (by larryv@…): The `arb` port already contains a file named [[source:trunk/dports/science/arb/files/patch-ARB-makefile.diff|patch-ARB- makefile.diff]], but it doesn’t seem to be used. Would it be okay if I overwrote that one? -- Ticket URL: <https://trac.macports.org/ticket/38204#comment:2> MacPorts <http://www.macports.org/> Ports system for Mac OS
#38204: arb @5.5: Disable compiler optimization to fix runtime crash of fast aligner ------------------------------+--------------------------------- Reporter: matt.cottrell@… | Owner: larryv@… Type: defect | Status: assigned Priority: Normal | Milestone: Component: ports | Version: Resolution: | Keywords: maintainer haspatch Port: arb | ------------------------------+--------------------------------- Comment (by matt.cottrell@…): Replying to [comment:2 larryv@…]:
The `arb` port already contains a file named [[source:trunk/dports/science/arb/files/patch-ARB-makefile.diff|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 -- Ticket URL: <https://trac.macports.org/ticket/38204#comment:3> MacPorts <http://www.macports.org/> Ports system for Mac OS
#38204: arb @5.5: Disable compiler optimization to fix runtime crash of fast aligner ------------------------------+--------------------------------- Reporter: matt.cottrell@… | Owner: larryv@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: Resolution: fixed | Keywords: maintainer haspatch Port: arb | ------------------------------+--------------------------------- Changes (by larryv@…): * status: assigned => closed * resolution: => fixed Comment: Committed in r103435. Thanks! -- Ticket URL: <https://trac.macports.org/ticket/38204#comment:4> MacPorts <http://www.macports.org/> Ports system for Mac OS
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