În mie., 2 ian. 2019 la 15:27, Gustavo Romero <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>> 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>> > > >> +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 > > -- 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 +1 480 627 9108 / +370 653 11125
