[med-svn] [Git][med-team/bowtie2][debian/experimental] 8 commits: Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Dec 26 16:36:32 GMT 2020
Michael R. Crusoe pushed to branch debian/experimental at Debian Med / bowtie2
Commits:
2a392383 by Andreas Tille at 2020-12-15T19:08:29+01:00
Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.
- - - - -
cffbcd98 by Andreas Tille at 2020-12-15T19:12:02+01:00
Force same hostname to enable reproducible builds
- - - - -
55996a0c by Andreas Tille at 2020-12-15T19:12:31+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
98654ead by Andreas Tille at 2020-12-15T19:12:31+01:00
routine-update: debhelper-compat 13
- - - - -
b6d914ea by Andreas Tille at 2020-12-15T20:56:12+01:00
use binaries installed to debian/tmp
- - - - -
0e91df1a by Andreas Tille at 2020-12-15T21:23:01+01:00
Upload to unstable
- - - - -
15221194 by Michael R. Crusoe at 2020-12-26T14:23:36+01:00
Experimental rebuild with libsimde-dev 0.7.0~rc-1
- - - - -
86ca8488 by Michael R. Crusoe at 2020-12-26T15:15:02+01:00
more LD_PRELOAD clearing
- - - - -
9 changed files:
- debian/bowtie2.install
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/use-source-date-epoch-in-Makefile.patch
- debian/rules
- debian/tests/binary-run
- debian/tests/check-wo-arguments
- debian/tests/indexing-ref-genome
Changes:
=====================================
debian/bowtie2.install
=====================================
@@ -1,9 +1 @@
-bowtie2 usr/bin
-bowtie2-align-l usr/bin
-bowtie2-align-s usr/bin
-bowtie2-build usr/bin
-bowtie2-build-l usr/bin
-bowtie2-build-s usr/bin
-bowtie2-inspect usr/bin
-bowtie2-inspect-l usr/bin
-bowtie2-inspect-s usr/bin
+usr/local/bin usr
=====================================
debian/changelog
=====================================
@@ -1,3 +1,25 @@
+bowtie2 (2.4.2-3~0exp0simde) experimental; urgency=medium
+
+ * Team upload.
+ * Experimental rebuild with libsimde-dev 0.7.0~rc-1
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sat, 26 Dec 2020 14:23:18 +0100
+
+bowtie2 (2.4.2-2) unstable; urgency=medium
+
+ [ Vagrant Cascadian ]
+ * Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.
+ Closes: #977435
+ * Force same hostname to enable reproducible builds
+ Closes: #977436
+
+ [ Andreas Tille ]
+ * Standards-Version: 4.5.1 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * use binaries installed to debian/tmp
+
+ -- Andreas Tille <tille at debian.org> Tue, 15 Dec 2020 21:07:56 +0100
+
bowtie2 (2.4.2-1) unstable; urgency=medium
* New upstream version 2.4.2
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Alexandre Mestiashvili <mestia at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
help2man,
libtbb-dev,
python3,
@@ -13,8 +13,8 @@ Build-Depends: debhelper-compat (= 12),
libclone-perl,
libfile-which-perl,
zlib1g-dev,
- libsimde-dev
-Standards-Version: 4.5.0
+ libsimde-dev (>= 0.7.0~rc-1)
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/bowtie2
Vcs-Git: https://salsa.debian.org/med-team/bowtie2.git
Homepage: http://bowtie-bio.sourceforge.net/bowtie2
=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ silence_tbb_deprecation_warning.patch
simde
correct_64bit_test
no_sanity
+use-source-date-epoch-in-Makefile.patch
=====================================
debian/patches/use-source-date-epoch-in-Makefile.patch
=====================================
@@ -0,0 +1,20 @@
+From: Vagrant Cascadian <vagrant at reproducible-builds.org>
+Subject: Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.
+Last-Update: Mon, 14 Dec 2020 19:56:00 -0800
+Bug-Debian: https://bugs.debian.org/977435
+
+https://reproducible-builds.org/docs/source-date-epoch/
+
+Index: bowtie2/Makefile
+===================================================================
+--- bowtie2.orig/Makefile
++++ bowtie2/Makefile
+@@ -279,7 +279,7 @@ both-debug: bowtie2-align-s-debug bowtie
+ DEFS := -fno-strict-aliasing \
+ -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" \
+ -DBUILD_HOST="\"$${HOSTNAME:-`hostname`}\"" \
+- -DBUILD_TIME="\"`date -u`\"" \
++ -DBUILD_TIME="\"`LC_ALL=C date -u -d@$(SOURCE_DATE_EPOCH)`\"" \
+ -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
+ $(FILE_FLAGS) \
+ $(PREF_DEF) \
=====================================
debian/rules
=====================================
@@ -24,7 +24,7 @@ export EXTRA_OPTIONS
dh $@
override_dh_auto_build:
- LD_PRELOAD= dh_auto_build -- EXTRA_FLAGS="-std=c++98 $(LDFLAGS)" $(EXTRA_OPTIONS)
+ LD_PRELOAD= dh_auto_build -- EXTRA_FLAGS="-std=c++98 $(LDFLAGS)" $(EXTRA_OPTIONS) HOSTNAME=reproducible-hostname
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
@@ -46,15 +46,15 @@ override_dh_install:
override_dh_installman:
mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
- debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"
- debian/help2man-wrapper $(pkg)-build "wrapper for $(pkg)-build-*"
- debian/help2man-wrapper $(pkg)-build-l "building a colorspace index for $(pkg)"
- debian/help2man-wrapper $(pkg)-build-s "building a colorspace index for $(pkg)"
- debian/help2man-wrapper $(pkg)-inspect "wrapper for $(pkg)-inspect-* index"
- debian/help2man-wrapper $(pkg)-inspect-l "extracts information from a $(pkg) index"
- debian/help2man-wrapper $(pkg)-inspect-s "extracts information from a $(pkg) index"
- debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
- debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
+ LD_PRELOAD= debian/help2man-wrapper $(pkg) "wrapper for $(pkg)-align-*"
+ LD_PRELOAD= debian/help2man-wrapper $(pkg)-build "wrapper for $(pkg)-build-*"
+ LD_PRELOAD= debian/help2man-wrapper $(pkg)-build-l "building a colorspace index for $(pkg)"
+ LD_PRELOAD= debian/help2man-wrapper $(pkg)-build-s "building a colorspace index for $(pkg)"
+ LD_PRELOAD= debian/help2man-wrapper $(pkg)-inspect "wrapper for $(pkg)-inspect-* index"
+ LD_PRELOAD= debian/help2man-wrapper $(pkg)-inspect-l "extracts information from a $(pkg) index"
+ LD_PRELOAD= debian/help2man-wrapper $(pkg)-inspect-s "extracts information from a $(pkg) index"
+ LD_PRELOAD= debian/help2man-wrapper $(pkg)-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
+ LD_PRELOAD= debian/help2man-wrapper $(pkg)-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences"
rm -f $(CURDIR)/debian/$(pkg)/usr/bin/bowtie2-buildc
override_dh_installchangelogs:
=====================================
debian/tests/binary-run
=====================================
@@ -1,6 +1,7 @@
#!/bin/sh
set -e
+export LD_PRELOAD=
pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`
for file in build align inspect
do
=====================================
debian/tests/check-wo-arguments
=====================================
@@ -1,5 +1,6 @@
#/bin/sh -e
+export LD_PRELOAD=
TMP="$(mktemp)"
# Run bowtie2 without any arguments and save stderr in a temporary file:
STDOUT="$(bowtie2 2> ${TMP})"
=====================================
debian/tests/indexing-ref-genome
=====================================
@@ -1,5 +1,6 @@
#!/bin/sh
+export LD_PRELOAD=
set -e
pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`
examplesdir=/usr/share/doc/$pkg/examples
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/compare/bfa6fdd071b32c7d7455e50e140628b95eb88833...86ca8488922f46052f07fb6b591e6bcd7e679e95
--
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/compare/bfa6fdd071b32c7d7455e50e140628b95eb88833...86ca8488922f46052f07fb6b591e6bcd7e679e95
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201226/30067d0e/attachment-0001.html>
More information about the debian-med-commit
mailing list