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>> 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.
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>>
> >> +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