Package: release.debian.org Severity: normal Tags: buster User: [email protected] Usertags: pu
htslib is not built for i386 on buster (due to autopkgtest problems), making python-cyvcf2:i386/python3-cyvcf2:i386 uninstallable in buster due to their dependency on libhts2:i386. -11 was the only release not built for i386, but that made it into buster. The autopkgtest was subsequently fixed in -12, so let's rebuild that for buster. The alternative would be to remove the i386 binaries from src:cyvcf2. Andreas
diff -Nru htslib-1.9/debian/changelog htslib-1.9/debian/changelog --- htslib-1.9/debian/changelog 2019-04-24 08:51:48.000000000 +0200 +++ htslib-1.9/debian/changelog 2021-04-09 11:27:05.000000000 +0200 @@ -1,3 +1,15 @@ +htslib (1.9-12~deb10u1) buster; urgency=medium + + * Rebuild for buster. + + -- Andreas Beckmann <[email protected]> Fri, 09 Apr 2021 11:27:05 +0200 + +htslib (1.9-12) unstable; urgency=medium + + * Fix for the autopkgtest on i386 means we can re-enable it! (Closes: #942580) + + -- Michael R. Crusoe <[email protected]> Mon, 09 Dec 2019 19:06:02 +0100 + htslib (1.9-11) unstable; urgency=medium * Install README at request of upstream diff -Nru htslib-1.9/debian/control htslib-1.9/debian/control --- htslib-1.9/debian/control 2019-04-24 08:51:48.000000000 +0200 +++ htslib-1.9/debian/control 2019-12-09 18:31:11.000000000 +0100 @@ -19,7 +19,7 @@ Homepage: https://github.com/samtools/htslib Package: libhts2 -Architecture: any-amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32 +Architecture: any Multi-Arch: same Section: libs Depends: ${misc:Depends}, @@ -39,7 +39,7 @@ new index and then for the old if the new index is absent. Package: libhts-dev -Architecture: any-amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32 +Architecture: any Multi-Arch: same Section: libdevel Depends: libhts2 (= ${binary:Version}), @@ -99,7 +99,7 @@ This package contains test files and scripts for the HTSlib. Package: tabix -Architecture: any-amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32 +Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends} Description: generic indexer for TAB-delimited genome position files diff -Nru htslib-1.9/debian/tests/run-unit-test htslib-1.9/debian/tests/run-unit-test --- htslib-1.9/debian/tests/run-unit-test 2019-04-24 08:51:48.000000000 +0200 +++ htslib-1.9/debian/tests/run-unit-test 2019-12-09 18:56:17.000000000 +0100 @@ -4,16 +4,23 @@ pkg="htslib" if [ "$AUTOPKGTEST_TMP" = "" ] ; then - AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) fi -cp -aL /usr/share/${pkg}-test/* $AUTOPKGTEST_TMP +cp -aL /usr/share/${pkg}-test/* "$AUTOPKGTEST_TMP" -cd $AUTOPKGTEST_TMP +cd "$AUTOPKGTEST_TMP" sed -i 's#\$(HTSPREFIX)#/usr/include/#g' htslib_vars.mk sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk -CFLAGS="-O2 -fno-strict-aliasing -fno-code-hoisting" make -e check +CFLAGS="-O2 -fno-strict-aliasing -fno-code-hoisting" + +if grep sse /proc/cpuinfo > /dev/null; then + CFLAGS+=" -msse -mfpmath=sse" +fi +export CFLAGS + +make -e check echo "PASS" diff -Nru htslib-1.9/debian/upstream/metadata htslib-1.9/debian/upstream/metadata --- htslib-1.9/debian/upstream/metadata 2019-04-24 08:51:48.000000000 +0200 +++ htslib-1.9/debian/upstream/metadata 2019-12-06 18:52:51.000000000 +0100 @@ -1,15 +1,21 @@ Reference: - Author: "Heng Li" - Title: "Tabix: fast retrieval of sequence features from generic TAB-delimited files" - Journal: Bioinformatics - Year: 2011 - Volume: 27 - Number: 5 - Pages: 718-719 - DOI: 10.1093/bioinformatics/btq671 - PMID: 21208982 - URL: https://academic.oup.com/bioinformatics/article/27/5/718/262743/Tabix-fast-retrieval-of-sequence-features-from - eprint: https://academic.oup.com/bioinformatics/article-pdf/27/5/718/5504485/btq671.pdf + Author: "Heng Li" + Title: > + Tabix: fast retrieval of sequence features from generic TAB-delimited + files + Journal: Bioinformatics + Year: 2011 + Volume: 27 + Number: 5 + Pages: 718-719 + DOI: 10.1093/bioinformatics/btq671 + PMID: 21208982 + URL: "https://academic.oup.com/bioinformatics/article/27/5/718/262743/\ + Tabix-fast-retrieval-of-sequence-features-from" + ePrint: "https://academic.oup.com/bioinformatics/article-pdf/\ + 27/5/718/5504485/btq671.pdf" Registry: - Name: OMICtools - Entry: OMICS_13459 + - Name: OMICtools + Entry: OMICS_13459 + - Name: conda:bioconda + Entry: htslib
