[med-svn] [Git][med-team/bowtie2][master] 6 commits: Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.

[Andreas Tille]

Andreas Tille pushed to branch master 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

- - - - -


6 changed files:

- debian/bowtie2.install
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/use-source-date-epoch-in-Makefile.patch
- debian/rules


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 +1,18 @@
+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,
@@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 12),
                libfile-which-perl,
                zlib1g-dev,
                libsimde-dev
-Standards-Version: 4.5.0
+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)))



View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/compare/d81f9a835181d06d1ab4f4c1ae0233efe4b3ae0e...0e91df1ae1fad5da9353f7e386967b911c06446a

-- 
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/compare/d81f9a835181d06d1ab4f4c1ae0233efe4b3ae0e...0e91df1ae1fad5da9353f7e386967b911c06446a
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