[Debian-med-packaging] Bug#1033089: subread: reproducible-builds: Embedded build path in various binaries

[Vagrant Cascadian]

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