Bug#986669: buster-pu: package htslib/1.9-12~deb10u1
Package: release.debian.org
Severity: normal
Tags: buster
User: release.debian.org@packages.debian.org
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 <anbe@debian.org> 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 <michael.crusoe@gmail.com> 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
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