[med-svn] [Git][med-team/plink1-9][master] 8 commits: d/control: build depends on libsimde-dev.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Tue May 13 19:40:32 BST 2025
Étienne Mollier pushed to branch master at Debian Med / plink1.9
Commits:
ad144fb6 by Étienne Mollier at 2025-05-13T19:29:45+02:00
d/control: build depends on libsimde-dev.
- - - - -
eb444e53 by Étienne Mollier at 2025-05-13T19:32:36+02:00
handle-sse2.patch: use the system's libsimde-dev.
Closes: #1105180
- - - - -
44bfcbe1 by Étienne Mollier at 2025-05-13T20:00:05+02:00
d/{control,rules}: populate Built-Using with simde version.
This is needed for GPL-3 compliance.
- - - - -
155acad2 by Étienne Mollier at 2025-05-13T20:05:39+02:00
d/copyright: update the FSF contact address.
- - - - -
75040e13 by Étienne Mollier at 2025-05-13T20:31:16+02:00
d/control: append support for architecture arm64.
- - - - -
13a424b1 by Étienne Mollier at 2025-05-13T20:31:44+02:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
173d8695 by Étienne Mollier at 2025-05-13T20:35:37+02:00
d/copyright: also update FSF address for LGPL.
Gbp-Dch: ignore
- - - - -
5e5efa56 by Étienne Mollier at 2025-05-13T20:40:04+02:00
d/changelog: ready for upload to unstable.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/handle-sse2.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+plink1.9 (1.90~b7.7-241022-2) unstable; urgency=medium
+
+ * Team upload.
+ * d/control: build depends on libsimde-dev.
+ * handle-sse2.patch: use the system's libsimde-dev.
+ * d/control: append support for architecture arm64. (Closes: #1105180)
+ * d/{control,rules}: populate Built-Using with simde version.
+ This is needed for GPL-3 compliance.
+ * d/copyright: update the FSF contact address.
+ * d/control: declare compliance to standards version 4.7.2.
+
+ -- Étienne Mollier <emollier at debian.org> Tue, 13 May 2025 20:32:04 +0200
+
plink1.9 (1.90~b7.7-241022-1) unstable; urgency=medium
* New upstream version 1.90~b7.7-241022
=====================================
debian/control
=====================================
@@ -6,18 +6,24 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
libblas-dev | libblas.so,
liblapack-dev | liblapack.so,
+ libsimde-dev,
zlib1g-dev
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/plink1-9
Vcs-Git: https://salsa.debian.org/med-team/plink1-9.git
Homepage: https://www.cog-genomics.org/plink/1.9/
Rules-Requires-Root: no
Package: plink1.9
-Architecture: any-amd64 any-i386 armel armhf mipsel
+# FIXME: since enabling the ability to use simde, it may be possible to
+# extend to Architecture: any, but it may be preferrable to wait for
+# after forky release, in order to avoid running into build success
+# resulting in autopkgtest failures.
+Architecture: any-amd64 any-i386 arm64 armel armhf mipsel
Depends: ${misc:Depends},
${shlibs:Depends}
Recommends: libopenblas0 | libblis4
+Built-Using: ${simde:Built-Using}
Description: whole-genome association analysis toolset
plink expects as input the data from SNP (single nucleotide polymorphism)
chips of many individuals and their phenotypical description of a disease.
=====================================
debian/copyright
=====================================
@@ -77,8 +77,7 @@ License: GPL-3
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ along with this package; if not, see <https://www.gnu.org/licenses/>.
.
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL-3'.
@@ -95,8 +94,7 @@ License: GPL-3+
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ along with this package; if not, see <https://www.gnu.org/licenses/>.
.
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL-3'.
@@ -149,8 +147,7 @@ License: LGPL-2.1
GNU Lesser General Public License for more details.
.
You should have received a copy of the GNU Lesser General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
+ along with this program; if not, see <https://www.gnu.org/licenses/>.
.
On Debian systems, the complete text of the GNU Lesser General
Public License can be found in `/usr/share/common-licenses/LGPL-2.1'.
=====================================
debian/patches/handle-sse2.patch
=====================================
@@ -0,0 +1,34 @@
+Description: use the system's simde library.
+ This allows building plink1.9 for arm64 (and probably other
+ architectures too).
+ .
+ Forwarding upstream is not needed because they use an embedded copy of
+ simde instead of the operating system's.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1105180
+Forwarded: not-needed
+Last-Update: 2025-05-13
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- plink1-9.orig/SFMT.h
++++ plink1-9/SFMT.h
+@@ -133,7 +133,7 @@
+ #include <emmintrin.h>
+ #else
+ #define SIMDE_ENABLE_NATIVE_ALIASES
+- #include "x86/sse2.h"
++ #include <simde/x86/sse2.h>
+ #endif
+
+ /** 128-bit data structure */
+--- plink1-9.orig/plink_common.h
++++ plink1-9/plink_common.h
+@@ -191,7 +191,7 @@
+ #include <emmintrin.h>
+ #else
+ #define SIMDE_ENABLE_NATIVE_ALIASES
+- #include "x86/sse2.h"
++ #include <simde/x86/sse2.h>
+ #endif
+
+ #define VECFTYPE __m128
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
fix_makefile.patch
blas.patch
+handle-sse2.patch
=====================================
debian/rules
=====================================
@@ -31,6 +31,14 @@ override_dh_installman:
override_dh_installchangelogs:
dh_installchangelogs debian/upstream.docs/upstream.changelog
+SIMDE_VERSION=$(shell \
+ dpkg-query \
+ -f '$${source:Package} (= $${source:Version}), ' \
+ -W "libsimde-dev" \
+)
+override_dh_gencontrol:
+ dh_gencontrol -- -Vsimde:Built-Using="$(SIMDE_VERSION)"
+
# Upstream provides unversioned download thus we need to read the version out of the source code
get-orig-source:
. debian/get-orig-source
View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/compare/2f36c0c90fe8add0533dafef159e86c3a119d0cf...5e5efa567c9dab3c66e08bd0b21f3041ba2d46eb
--
View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/compare/2f36c0c90fe8add0533dafef159e86c3a119d0cf...5e5efa567c9dab3c66e08bd0b21f3041ba2d46eb
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