În mie., 2 ian. 2019 la 15:27, Gustavo Romero <grom...@linux.vnet.ibm.com
<mailto:grom...@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 <grom...@linux.vnet.ibm.com
<mailto:grom...@linux.vnet.ibm.com> <mailto:grom...@linux.vnet.ibm.com
<mailto:grom...@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>
> >> m...@commonwl.org <mailto:m...@commonwl.org> <mailto:m...@commonwl.org
<mailto:m...@commonwl.org>> <mailto:m...@commonwl.org <mailto:m...@commonwl.org> <mailto:m...@commonwl.org
<mailto:m...@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>
> m...@commonwl.org <mailto:m...@commonwl.org> <mailto:m...@commonwl.org
<mailto:m...@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>
m...@commonwl.org <mailto:m...@commonwl.org>
+1 480 627 9108 / +370 653 11125
