Re: Help requested for htslib build failure on ppc64el
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.
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?
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
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