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Bug#986669: marked as done (buster-pu: package htslib/1.9-12~deb10u1)

Your message dated Sat, 09 Oct 2021 12:11:43 +0100
with message-id <896b7609401ceb0e1c537222e26587ea2351415d.camel@adam-barratt.org.uk>
and subject line Closing bugs for fixes included in the 10.11 point release
has caused the Debian Bug report #986669,
regarding buster-pu: package htslib/1.9-12~deb10u1
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
986669: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=986669
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
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

--- End Message ---
--- Begin Message --- 
Package: release.debian.org
Version: 10.11

Hi,

The updates relating to these bugs were included in this morning's
10.11 point release for buster.

Regards,

Adam

--- End Message ---
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