https://buildd.debian.org/status/package.php?p=htslib&suite=experimental
http://metadata.ftp-master.debian.org/changelogs/main/h/htslib/htslib_1.9-9~floatingpoint0_changelog Seems to work after all! Maybe a qemu bug? -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project https://impactstory.org/u/0000-0002-2961-9670 m...@commonwl.org În mie., 9 ian. 2019, 19:38 Gustavo Romero <grom...@linux.vnet.ibm.com a scris: > 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 < > 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 > > > >
