Ping.
On 01/04/2019 08:01 PM, Gustavo Romero wrote:
> Hi Michael,
>
> Thanks for the diff and the additional information on the failure.
>
> Since I could not reproduce the issue locally, would you mind to point a buildd machine (I tried the buildd logs for htslib without success) where it fails, please?
>
> Thank you.
>
> Regards,
> Gustavo
>
> On 01/02/2019 02:41 PM, Michael Crusoe wrote:
>>
>>
>> În mie., 2 ian. 2019 la 15:27, Gustavo Romero <gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com>> a scris:
>>
>> Hello Michael,
>>
>> On 12/31/2018 02:50 PM, Michael Crusoe wrote:
>> > În lun., 31 dec. 2018 la 06:42, Gustavo Romero <gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com> <mailto:gromero@linux.vnet.ibm.com <mailto:gromero@linux.vnet.ibm.com>>> a scris:
>> > diff --git a/sam.c b/sam.c
>> > index aa94776..23233a0 100644
>> > --- a/sam.c
>> > +++ b/sam.c
>> > @@ -1408,7 +1408,7 @@ int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b)
>> > else if (type == 'S') while (q + 1 < p) { u16_to_le(strtoul(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 2; _skip_to_comma(q, p); }
>> > else if (type == 'i') while (q + 1 < p) { i32_to_le(strtol(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
>> > else if (type == 'I') while (q + 1 < p) { u32_to_le(strtoul(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
>> > - else if (type == 'f') while (q + 1 < p) { float_to_le(strtod(q + 1, &q), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
>> > + else if (type == 'f') while (q + 1 < p) { float_to_le(strtof(q + 1, &q), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
>> > else _parse_err_param(1, "unrecognized type B:%c", type);
>> >
>> > #undef _skip_to_comma
>> >
>> >
>> > Applying this patch and compiling under a qemu-based sid-ppc64el builder gets us to only a single test failure (yay!)
>> >
>> > ===
>> > test_vcf_various:
>> > /build/htslib-1.9/htsfile -c /build/htslib-1.9/test/formatcols.vcf
>> > The outputs differ:
>> > /build/htslib-1.9/test/formatcols.vcf
>> > /build/htslib-1.9/test/formatcols.vcf.new
>> > .. failed ...
>> > ===
>>
>> Thanks for testing it!
>>
>> hmm right... I'm not able to reproduce that failure on my setup.
>>
>>
>> I've added the patch our git repo, so maybe try again by upcommenting it at https://salsa.debian.org/med-team/htslib/blob/master/debian/patches/series ?
>>
>>
>> Could you share the differences when it fails? I think a 'diff -u formatcols.vcf formatcols.vcf.new' suffices.
>>
>> root@mrcdev:/build/htslib-1.9# diff -u /build/htslib-1.9/test/formatmissing-out.vcf /build/htslib-1.9/test/formatmissing-out.vcf.new
>> --- /build/htslib-1.9/test/formatmissing-out.vcf 2018-07-18 08:33:10.000000000 +0000
>> +++ /build/htslib-1.9/test/formatmissing-out.vcf.new 2019-01-02 16:14:27.000000000 +0000
>> @@ -3,4 +3,4 @@
>> ##contig=<ID=1>
>> ##FORMAT=<ID=S,Number=1,Type=String,Description="Text">
>> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3
>> -1 100 a A T . . . . . . .
>> +1 100 a A T 3.40282e+38 . . . . . .
>>
>> root@mrcdev:/build/htslib-1.9# diff -u /build/htslib-1.9/test/formatcols.vcf /build/htslib-1.9/test/formatcols.vcf.new
>> --- /build/htslib-1.9/test/formatcols.vcf 2018-07-18 08:33:10.000000000 +0000
>> +++ /build/htslib-1.9/test/formatcols.vcf.new 2019-01-02 16:14:27.000000000 +0000
>> @@ -3,4 +3,4 @@
>> ##contig=<ID=1>
>> ##FORMAT=<ID=S,Number=1,Type=String,Description="Text">
>> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3
>> -1 100 a A T . . . S a bbbbbbb ccccccccc
>> +1 100 a A T 3.40282e+38 . . S a bbbbbbb ccccccccc
>>
>> > In the meantime, to unclog a chain of packages that have been held back from migrating to testing, I've uploaded a version of the package that uses -O0 for ppc64el only; which I agree is not ideal.
>> >
>> > If you think this is a qemu-only test failure then I can upload a build to experimental so that real hardware is used (I don't have porter box access)
>>
>> I don't know... but all debugging / testing at my side is on a ppc64el VM (qemu/kvm-only so), so probably not a VM vs baremetal issue.
>>
>> Did you check if the same error happens on x86_64 when that patch is applied? Or it's still ppc64el-specific?
>>
>>
>> amd64 builds just fine with the patch
>>
>> Cheers,
>> Gustavo
>> >
>> > Cheers,
>> > Gustavo
>> >
>> > > Cheers,
>> > >
>> > > Steffen
>> > >
>> > > On 27.12.18 15:41, Michael Crusoe wrote:
>> > >> https://buildd.debian.org/status/fetch.php?pkg=htslib&arch=ppc64el&ver=1.9-7&stamp=1545236716&raw=0
>> > >>
>> > >> Can I get some assistance here? Rebuilding using Qemu and the earlier source packages produces the same error, so maybe this is a regression in the compiler?
>> > >>
>> > >> --
>> > >> Michael R. Crusoe
>> > >> Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/>
>> > >> Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
>> > >> https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670>
>> > >> mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>>>
>> > >> +1 480 627 9108 / +370 653 11125
>> > >
>> >
>> >
>> >
>> > --
>> > Michael R. Crusoe
>> > Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/>
>> > Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
>> > https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670>
>> > mrc@commonwl.org <mailto:mrc@commonwl.org> <mailto:mrc@commonwl.org <mailto:mrc@commonwl.org>>
>> > +1 480 627 9108 / +370 653 11125
>>
>>
>>
>> --
>> Michael R. Crusoe
>> Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/>
>> Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
>> https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670>
>> mrc@commonwl.org <mailto:mrc@commonwl.org>
>> +1 480 627 9108 / +370 653 11125
>