Debian Bug report logs - #977435
bowtie2: reproducible builds: Embeds timestamp in build

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Vagrant Cascadian <vagrant@reproducible-builds.org>

To: submit@bugs.debian.org

Subject: bowtie2: reproducible builds: Embeds timestamp in build

Date: Mon, 14 Dec 2020 19:56:00 -0800

[Message part 1 (text/plain, inline)]

Source: bowtie2
Severity: normal
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: timestamps
X-Debbugs-Cc: reproducible-bugs@lists.alioth.debian.org

The debugging symbols embed the build time:

  https://tests.reproducible-builds.org/debian/rb-pkg/bullseye/amd64/diffoscope-results/bowtie2.html

  ./usr/lib/debug/.dwz/x86_64-linux-gnu/bowtie2.debug 
  501 	··[··2df6]··BUILD_TIME·"Thu·Dec·10·16:47:13·UTC·2020"
  504 	··[··2f02]··BUILD_TIME·"Thu·Jan·13·00:06:51·UTC·2022"

The attached patch fixes this by adjusting the Makefile to have date to
produce a consistent timestamp using SOURCE_DATE_EPOCH.


Thanks for maintaining bowtie2!


live well,
  vagrant

[0001-debian-patches-Patch-Makefile-to-use-SOURCE_DATE_EPO.patch (text/x-diff, inline)]

From abf1a60be6d2bf1b2d86cc66a001f1d233e3d2da Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@reproducible-builds.org>
Date: Tue, 15 Dec 2020 03:41:17 +0000
Subject: [PATCH 1/2] debian/patches: Patch Makefile to use SOURCE_DATE_EPOCH.

---
 debian/patches/series                          |  1 +
 .../patches/use-source-date-epoch-in-Makefile  | 18 ++++++++++++++++++
 2 files changed, 19 insertions(+)
 create mode 100644 debian/patches/use-source-date-epoch-in-Makefile

diff --git a/debian/patches/series b/debian/patches/series
index e11a345..d85c587 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -8,3 +8,4 @@ silence_tbb_deprecation_warning.patch
 simde
 correct_64bit_test
 no_sanity
+use-source-date-epoch-in-Makefile
diff --git a/debian/patches/use-source-date-epoch-in-Makefile b/debian/patches/use-source-date-epoch-in-Makefile
new file mode 100644
index 0000000..a37f05c
--- /dev/null
+++ b/debian/patches/use-source-date-epoch-in-Makefile
@@ -0,0 +1,18 @@
+From: Vagrant Cascadian <vagrant@reproducible-builds.org>
+Subject: Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.
+
+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) \
-- 
2.29.2

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Message #10 received at 977435-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>

To: 977435-close@bugs.debian.org

Subject: Bug#977435: fixed in bowtie2 2.4.2-2

Date: Tue, 15 Dec 2020 21:03:44 +0000

Source: bowtie2
Source-Version: 2.4.2-2
Done: Andreas Tille <tille@debian.org>

We believe that the bug you reported is fixed in the latest version of
bowtie2, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 977435@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated bowtie2 package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Tue, 15 Dec 2020 21:07:56 +0100
Source: bowtie2
Architecture: source
Version: 2.4.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 977435 977436
Changes:
 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
Checksums-Sha1:
 87abc770a18abb58d0058d82099e263e8c40e3b7 2350 bowtie2_2.4.2-2.dsc
 d8fdf2f300a2f0a52183b2ca753c4ac724825c05 17536 bowtie2_2.4.2-2.debian.tar.xz
 8c63ef480352ee8a389f3eb9de4e622210ba4193 7032 bowtie2_2.4.2-2_amd64.buildinfo
Checksums-Sha256:
 2e82e1a135213c60b3e7741f86df9a48a98f09385a90911f11e44e657664aa94 2350 bowtie2_2.4.2-2.dsc
 2bb28268081cf0f96524e51d647743f28c9b44aee6b8e6d0d7a9bc960057fffe 17536 bowtie2_2.4.2-2.debian.tar.xz
 f49d4bb3bd61e17b7b69356060d39578b1e7897f882020989aac94a541f38e7a 7032 bowtie2_2.4.2-2_amd64.buildinfo
Files:
 8ba86af5d67d1cf3ce6e383d08cae313 2350 science optional bowtie2_2.4.2-2.dsc
 711d0c1b45ef9f175e04af81fd523d0a 17536 science optional bowtie2_2.4.2-2.debian.tar.xz
 af046a86e3ea61b045c2a9b3da83acbd 7032 science optional bowtie2_2.4.2-2_amd64.buildinfo

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