From mboxrd@z Thu Jan  1 00:00:00 1970
From: Andreas Enge <andreas@enge.fr>
Subject: bug#19708: Bowtie fails to build
Date: Wed, 28 Jan 2015 17:57:35 +0100
Message-ID: <20150128165735.GA14986@debian.math.u-bordeaux1.fr>
References: <20150127214727.GA6287@debian>
	<idjwq476lmt.fsf@bimsb-sys02.mdc-berlin.net>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Return-path: <bug-guix-bounces+gcggb-bug-guix=m.gmane.org@gnu.org>
Received: from eggs.gnu.org ([2001:4830:134:3::10]:36599)
	by lists.gnu.org with esmtp (Exim 4.71)
	(envelope-from <Debian-debbugs@debbugs.gnu.org>) id 1YGVwN-0007IB-R8
	for bug-guix@gnu.org; Wed, 28 Jan 2015 11:58:08 -0500
Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71)
	(envelope-from <Debian-debbugs@debbugs.gnu.org>) id 1YGVwL-0002ae-0A
	for bug-guix@gnu.org; Wed, 28 Jan 2015 11:58:07 -0500
Received: from debbugs.gnu.org ([140.186.70.43]:40482)
	by eggs.gnu.org with esmtp (Exim 4.71)
	(envelope-from <Debian-debbugs@debbugs.gnu.org>) id 1YGVwK-0002aX-SN
	for bug-guix@gnu.org; Wed, 28 Jan 2015 11:58:04 -0500
Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.80)
	(envelope-from <Debian-debbugs@debbugs.gnu.org>) id 1YGVwJ-0000l2-Gs
	for bug-guix@gnu.org; Wed, 28 Jan 2015 11:58:03 -0500
Sender: "Debbugs-submit" <debbugs-submit-bounces@debbugs.gnu.org>
Resent-Message-ID: <handler.19708.B19708.14224642682861@debbugs.gnu.org>
Content-Disposition: inline
In-Reply-To: <idjwq476lmt.fsf@bimsb-sys02.mdc-berlin.net>
List-Id: Bug reports for GNU Guix <bug-guix.gnu.org>
List-Unsubscribe: <https://lists.gnu.org/mailman/options/bug-guix>,
	<mailto:bug-guix-request@gnu.org?subject=unsubscribe>
List-Archive: <http://lists.gnu.org/archive/html/bug-guix>
List-Post: <mailto:bug-guix@gnu.org>
List-Help: <mailto:bug-guix-request@gnu.org?subject=help>
List-Subscribe: <https://lists.gnu.org/mailman/listinfo/bug-guix>,
	<mailto:bug-guix-request@gnu.org?subject=subscribe>
Errors-To: bug-guix-bounces+gcggb-bug-guix=m.gmane.org@gnu.org
Sender: bug-guix-bounces+gcggb-bug-guix=m.gmane.org@gnu.org
To: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Cc: 19708@debbugs.gnu.org

On Wed, Jan 28, 2015 at 03:11:06PM +0100, Ricardo Wurmus wrote:
> Whether or not a platform is 64-bit is determined with uname.  Both
> these errors relate to using uname.

Clearly, only x86_64 is supported. Citing from Makefile:
BITS=32
ifeq (x86_64,$(shell uname -m))
        BITS=64
endif
# msys will always be 32 bit so look at the cpu arch instead.
ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
        ifeq (1,$(MINGW))
                BITS=64
        endif
endif
ifeq (32,$(BITS))
  $(error bowtie2 compilation requires a 64-bit platform )
endif

So we should disable mips and i686.


> This is odd.  The Makefile only adds this option on MacOS:
>     MACOS = 0
>     ifneq (,$(findstring Darwin,$(shell uname)))
>             MACOS = 1
>             ifneq (,$(findstring 13,$(shell uname -r)))
>                     CPP = clang++
>                     CC = clang
>                     EXTRA_FLAGS += -stdlib=libstdc++
>             endif
>     endif

I see the following in my Makefile:
MACOS = 0
ifneq (,$(findstring Darwin,$(shell uname)))
        MACOS = 1
endif

ifneq (,$(findstring 13,$(shell uname -r)))
        CPP = clang++
        CC = clang
        EXTRA_FLAGS += -stdlib=libstdc++
endif

Notice the different placements of the "endif". Are we talking about different
versions of bowtie? I looked at the top Makefile from the result of
"guix build bowtie -S".

Andreas