Hi Andreas,

Note I ended pushing some changes to the repository after some
more verifications yesterday.

Andreas Tille, on 2020-10-13 09:06:52 +0200:
> Hmmmm, may be I should remove third_party/cpuid.h in general?
> Given its copyright informazion is
>     Copyright (C) 2007, 2008, 2009 Free Software Foundation, Inc.
> that seems to be a pretty old copy of this file.

I can confirm excluding third_party/cpuid.h does the job.

> > > [1] 
> > > https://salsa.debian.org/med-team/bowtie/-/blob/master/debian/patches/popcnt_capability.patch
> > 
> > As a side note, I believe that the $(filter ...) statement added
> > in the patch to be able to list architectures reverted the
> > logic, so replaced the ifeq (...) statement to an ifneq (...).
> > 
> > Most changes are available on my machine.  I would have
> > suggested to push them, but my build targeting mips64el failed
> > and it seems that its because `uname -m` returns mips64 on that
> > architecture.  I'm not 100% sure of the name for the other
> > architectures, maybe listing CPUs handling popcnt might be
> > simpler ?
> > 
> > Anyway in hope any of these ideas helps...
> 
> Would you mind sending a `git diff` to make sure I fully
> understood what you mean?

The diff below shows what I pushed to salsa yesterday; it is a
bit different from my statement in my email, as I filter out
x86_64 for setting POPCNT_CAPABILITY=0 instead of listing
architectures that do not have this available:

-------8<--------------8<--------------8<--------------8<-------
commit ebb4152dc649d63bec2360a21bd909f1d4a44d2a
Author: Étienne Mollier <etienne.moll...@mailoo.org>
Date:   Mon Oct 12 23:43:50 2020 +0200

    reviewed debian/patches/popcnt_capability

diff --git a/debian/patches/popcnt_capability.patch 
b/debian/patches/popcnt_capability.patch
index eb0ae56..863c936 100644
--- a/debian/patches/popcnt_capability.patch
+++ b/debian/patches/popcnt_capability.patch
@@ -1,6 +1,7 @@
 Description: Set POPCNT_CAPABILITY=0 for more architectures than just aarch64
 Bug-Debian: https://bugs.debian.org/972004
 Author: Andreas Tille <ti...@debian.org>
+Reviewed-By: Étienne Mollier <etienne.moll...@mailoo.org>
 Last-Update: Mon, 12 Oct 2020 11:29:03 +0200
 
 --- a/Makefile
@@ -10,7 +11,7 @@ Last-Update: Mon, 12 Oct 2020 11:29:03 +0200
  
  POPCNT_CAPABILITY ?= 1
 -ifeq (aarch64,$(shell uname -m))
-+ifeq (,$(filter $(shell uname -m), aarch64 alpha mips64el ppc64 ppc64el 
risc64 sparc64 x32))
++ifeq (,$(filter $(shell uname -m), x86_64))
        POPCNT_CAPABILITY=0
  endif
  ifeq (1, $(POPCNT_CAPABILITY))
-------8<--------------8<--------------8<--------------8<-------

If you think some more architectures can make use of popcnt,
they can be appended next to x86_64.  If you want to make sure
the option is applied, check the build log, the compilation
command should show -DPOPCNT_CAPABILITY.

Have a nice day,
-- 
Étienne Mollier <etienne.moll...@mailoo.org>
Old rsa/3072: 5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
New rsa/4096: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/tty1, please excuse my verbosity.

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