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)
Change History (6)
Changed 12 years ago by mattcottrell
| Attachment: | Portfile.diff added |
|---|
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: | new → assigned |
| Summary: | Reduce compiler optimization to fix arb runtime crash of fast aligner → arb @5.5: Disable compiler optimization to fix runtime crash of fast aligner |
| Version: | 2.1.3 |
Thanks.
comment:2 follow-up: 3 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 Changed 12 years ago by mattcottrell
Replying to larryv@…:
The
arbport 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: | assigned → closed |
Committed in r103435. Thanks!
Portfile diff reduces compiler optimization