From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Andreas Enge <andreas@enge.fr>
Cc: 19708@debbugs.gnu.org
Subject: bug#19708: Bowtie fails to build
Date: Thu, 29 Jan 2015 11:01:56 +0100 [thread overview]
Message-ID: <idjpp9x7vmz.fsf@bimsb-sys02.mdc-berlin.net> (raw)
In-Reply-To: <20150128165735.GA14986@debian.math.u-bordeaux1.fr>
Andreas Enge writes:
> 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))
> $(error bowtie2 compilation requires a 64-bit platform )
> endif
>
> So we should disable mips and i686.
Submitted a patch to the ML to do just that.
>> This is odd. The Makefile only adds this option on MacOS:
>> MACOS = 0
>> ifneq (,$(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,$(shell uname -r)))
> CPP = clang++
> CC = clang
> EXTRA_FLAGS += -stdlib=libstdc++
> endif
>
> Notice the different placements of the "endif". Are we talking about different
> versions of bowtie? I looked at the top Makefile from the result of
> "guix build bowtie -S".
Oh, I must have been looking at master. In commit 4a99b0023[1] this was
changed to:
MACOS = 0
ifneq (,$(findstring Darwin,$(shell uname)))
MACOS = 1
ifneq (,$(findstring 13,$(shell uname -r)))
CPP = clang++
CC = clang
EXTRA_FLAGS += -stdlib=libstdc++
endif
endif
I'm not sure why it built the first time, though. (Compare [2] and
[3], both using the same release.) Anyway, I can go ahead and patch the
Makefile until a new release is out.
What do you think?
~~ Ricardo
[1]: https://github.com/BenLangmead/bowtie2/commit/4a99b0023bdfbbe486b9649489a32ea184c18c9a
[2]: http://hydra.gnu.org/build/175069
[3]: http://hydra.gnu.org/build/204787
next prev parent reply other threads:[~2015-01-29 10:03 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-01-27 21:47 bug#19708: Bowtie fails to build Andreas Enge
2015-01-28 14:11 ` Ricardo Wurmus
2015-01-28 16:57 ` Andreas Enge
2015-01-29 10:01 ` Ricardo Wurmus [this message]
2015-01-30 16:07 ` Mark H Weaver
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