Re: Does bwa really need to be limited to amd64?
على الجمعـة 8 نيسـان 2016 23:32، كتب Andreas Tille: >>> In any case, for most bioinformatics software that is now developed on >>> amd64, I >>> > > would not trust output of the programs built successfully on other >>> > > architectures unless there are good regression tests. >> > >> > That's a good point. Thanks for clarifying the situation anyway. > May be you can give some hints for such a test to our GSoC students? > I think any regression test should do the job. If you're asking about general hints, I'd say that looking in a tool's publication to see how it was validated it there could give a good idea about the kind of test that should be performed. Then it's just a matter of automating that. That's just my suggestion... Thanks and regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Re: Does bwa really need to be limited to amd64?
On Fri, Apr 08, 2016 at 10:58:01PM -0700, Afif Elghraoui wrote: > > على الجمعـة 8 نيسـان 2016 05:22، كتب Charles Plessy: > > > > In any case, for most bioinformatics software that is now developed on > > amd64, I > > would not trust output of the programs built successfully on other > > architectures unless there are good regression tests. > > That's a good point. Thanks for clarifying the situation anyway. May be you can give some hints for such a test to our GSoC students? > > So I take the opportunity to say a big thank you to the people working on > > regression tests right now :) > > Indeed. +1 :-) Kind regards Andreas. -- http://fam-tille.de
Re: Does bwa really need to be limited to amd64?
على الجمعـة 8 نيسـان 2016 05:22، كتب Charles Plessy: > BWA failed to build on i386 at version 0.7.5a-1 with the following error, > despite the -D_NO_SSE2 option: > > /usr/lib/gcc/i486-linux-gnu/4.7/include/emmintrin.h:32:3: error: #error > "SSE2 instruction set not enabled" > > https://buildd.debian.org/status/fetch.php?pkg=bwa=i386=0.7.5a-1=1370353173 > > I expect that if you try to build it on i386, it will fail again. > > In any case, for most bioinformatics software that is now developed on amd64, > I > would not trust output of the programs built successfully on other > architectures unless there are good regression tests. > That's a good point. Thanks for clarifying the situation anyway. > So I take the opportunity to say a big thank you to the people working on > regression tests right now :) Indeed. regards Afif -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
Re: Does bwa really need to be limited to amd64?
Le Fri, Apr 08, 2016 at 01:04:15AM -0700, Afif Elghraoui a écrit : > > As I've mentioned before, I'm trying to get circlator into testing. I > requested of the release team to allow it to migrate despite it's being > uninstallable on i386 [1]. I was then asked if there was any way to fix > that, so I looked into the problematic dependencies. bwa is set to amd64 > and kfreebsd-amd64 only. > > When I looked through the changelog, this looked like it was done a few > years ago because of the need for SSE2. In the current debian/rules, I > see that SSE2 is only added if the architecture matches amd64, but I > don't see anything about this in the upstream Makefile or READMEs. > > I don't have a chance to test out a build right now, but does anyone see > a problem with expanding the architecture list? Hi Afif, BWA failed to build on i386 at version 0.7.5a-1 with the following error, despite the -D_NO_SSE2 option: /usr/lib/gcc/i486-linux-gnu/4.7/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled" https://buildd.debian.org/status/fetch.php?pkg=bwa=i386=0.7.5a-1=1370353173 I expect that if you try to build it on i386, it will fail again. In any case, for most bioinformatics software that is now developed on amd64, I would not trust output of the programs built successfully on other architectures unless there are good regression tests. So I take the opportunity to say a big thank you to the people working on regression tests right now :) Have a nice day, -- Charles
Does bwa really need to be limited to amd64?
Hi, all, As I've mentioned before, I'm trying to get circlator into testing. I requested of the release team to allow it to migrate despite it's being uninstallable on i386 [1]. I was then asked if there was any way to fix that, so I looked into the problematic dependencies. bwa is set to amd64 and kfreebsd-amd64 only. When I looked through the changelog, this looked like it was done a few years ago because of the need for SSE2. In the current debian/rules, I see that SSE2 is only added if the architecture matches amd64, but I don't see anything about this in the upstream Makefile or READMEs. I don't have a chance to test out a build right now, but does anyone see a problem with expanding the architecture list? Thanks and regards Afif 1. https://lists.debian.org/debian-release/2016/04/msg00198.html -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
