Hi all,

when trying to fix some packages that have recently become unreproducible after 
adding build path variations, I have noticed that a common case is that some of 
these variations make it into Makefiles that have been generated by automake 
from upstream’s Makefile.in. Some of these Makefiles are included in the 
packages in question, for instance to automate tests that most likely were 
intended by upstream to be run at build time.

However, since with the introduction of the new autopkgtests upstream’s test 
cases are often also installed in /usr/share/doc/…/examples, we see some cases 
of Makefiles containing build-specific directories ending up in binary 
packages, since the values for C(XX|PP)FLAGS etc. are propagated from the build 
environment into these files. An example is [1] where the value of CFLAGS is 
modified.

I have found some more instances, and I have added some workarounds removing 
these problematic fields from the Makefile [2] to let them use the default if 
required — however, I am wondering whether these Makefiles should be installed 
at all. Cleaning them up would add quite a bit of overhead to the d/rules in 
each case and I am quite doubtful users would ever touch these Makefiles (if 
they even work at all).
Any opinions or ideas?

Cheers
Sascha

[1] 
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/armhf/hmmer2.html
    HMMER3 (package hmmer) is also affected.
[2] 
https://anonscm.debian.org/cgit/debian-med/toppred.git/commit/?id=8e5b443c66d60de5487c6e526a57828ec5e6a19e

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