Debian Bug report logs - #1033089
subread: reproducible-builds: Embedded build path in various binaries

Reply or subscribe to this bug.

Toggle useless messages

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: subread: reproducible-builds: Embedded build path in various binaries

Date: Thu, 16 Mar 2023 22:04:38 -0700

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

Source: subread
Version: 2.0.4+dfsg-1
Severity: normal
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: buildpath
X-Debbugs-Cc: reproducible-bugs@lists.alioth.debian.org

The build path is embedded in various binaries:

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

  /usr/bin/exactSNP

  /build/1st/subread-2.0.4+dfsg/src/input-files.c:3084
  vs.
  /build/2/subread-2.0.4+dfsg/2nd/src/input-files.c:3084

The attached patch fixes this by patching src/Makefile.Linux to not
override the CFLAGS and CXXFLAGS variables, so that the default flags
include -ffile-prefix-map to avoid embedding the build path.

Earlier versions (e.g. 2.0.3* currently in bookworm) did pass the
default flags, so this is a regression from what is currently in
bookworm.

According to my local tests, with this patch applied subread should build
reproducibly on tests.reproducible-builds.org!

Thanks for maintaining subread!

live well,
  vagrant

[0001-src-Makefile.Linux-Do-not-set-CFLAGS-and-CXXFLAGS-to.patch (text/x-diff, inline)]

From 661536e4afcec2e40682257e5aba8119b46935d7 Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@reproducible-builds.org>
Date: Thu, 16 Mar 2023 21:51:54 -0700
Subject: [PATCH 1/3] src/Makefile.Linux: Do not set CFLAGS and CXXFLAGS to
 empty values.

---
 src/Makefile.Linux | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/Makefile.Linux b/src/Makefile.Linux
index 0571c1a..a6ec556 100644
--- a/src/Makefile.Linux
+++ b/src/Makefile.Linux
@@ -6,8 +6,6 @@ OPT_LEVEL = 3
 include makefile.version
 -include ~/.R/DBPZ_debug_makefile
 
-CXXFLAGS=
-CFLAGS=
 CCFLAGS += -O${OPT_LEVEL} -fsigned-char -Wall -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64 ${WARNING_LEVEL}
 LDFLAGS += ${STATIC_MAKE} -pthread -lz -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
 CFLAGS += ${CCFLAGS} -fmessage-length=0 -ggdb
-- 
2.39.2

[signature.asc (application/pgp-signature, inline)]

Send a report that this bug log contains spam.