GNU bug report logs - #19708
Bowtie fails to build

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Package: guix;

Reported by: Andreas Enge <andreas <at> enge.fr>

Date: Tue, 27 Jan 2015 21:48:01 UTC

Severity: normal

Done: Mark H Weaver <mhw <at> netris.org>

Bug is archived. No further changes may be made.

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Report forwarded to bug-guix <at> gnu.org:
bug#19708; Package guix. (Tue, 27 Jan 2015 21:48:02 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Enge <andreas <at> enge.fr>:
New bug report received and forwarded. Copy sent to bug-guix <at> gnu.org. (Tue, 27 Jan 2015 21:48:02 GMT) Full text and rfc822 format available.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: bug-guix <at> gnu.org
Subject: Bowtie fails to build
Date: Tue, 27 Jan 2015 22:47:27 +0100
Hello,

bowtie currently fails to build on all three architectures on hydra.

On i686, the error message is:
Makefile:146: *** bowtie2 compilation requires a 64-bit platform .  Stop.

Surprisingly, the same error message is shown on mip64el (!).
From its description, I do not expect users to run the program on mips,
so it might be the safest option to disable the build of these two
architectures.

On x86_64, the error message is
g++: error: unrecognized command line option '-stdlib=libstdc++'
See http://hydra.gnu.org/build/204787 .

Andreas





Information forwarded to bug-guix <at> gnu.org:
bug#19708; Package guix. (Wed, 28 Jan 2015 14:12:01 GMT) Full text and rfc822 format available.

Message #8 received at 19708 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
To: Andreas Enge <andreas <at> enge.fr>
Cc: 19708 <at> debbugs.gnu.org
Subject: Re: bug#19708: Bowtie fails to build
Date: Wed, 28 Jan 2015 15:11:06 +0100
Andreas Enge writes:
> bowtie currently fails to build on all three architectures on hydra.
>
> On i686, the error message is:
> Makefile:146: *** bowtie2 compilation requires a 64-bit platform .  Stop.
>
> Surprisingly, the same error message is shown on mip64el (!).
> From its description, I do not expect users to run the program on mips,
> so it might be the safest option to disable the build of these two
> architectures.
>
> On x86_64, the error message is
> g++: error: unrecognized command line option '-stdlib=libstdc++'
> See http://hydra.gnu.org/build/204787 .

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

Whether or not a platform is 64-bit is determined with uname.  Both
these errors relate to using uname.

Is it not available at build time?

I can build the package just fine with:

    guix build -S bowtie
    ...
    guix enviroment --pure bowtie
    make


~~ Ricardo




Information forwarded to bug-guix <at> gnu.org:
bug#19708; Package guix. (Wed, 28 Jan 2015 16:58:03 GMT) Full text and rfc822 format available.

Message #11 received at 19708 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
Cc: 19708 <at> debbugs.gnu.org
Subject: Re: bug#19708: Bowtie fails to build
Date: Wed, 28 Jan 2015 17:57:35 +0100
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





Information forwarded to bug-guix <at> gnu.org:
bug#19708; Package guix. (Thu, 29 Jan 2015 10:03:02 GMT) Full text and rfc822 format available.

Message #14 received at 19708 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
To: Andreas Enge <andreas <at> enge.fr>
Cc: 19708 <at> debbugs.gnu.org
Subject: Re: bug#19708: Bowtie fails to build
Date: Thu, 29 Jan 2015 11:01:56 +0100
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




Reply sent to Mark H Weaver <mhw <at> netris.org>:
You have taken responsibility. (Fri, 30 Jan 2015 16:08:02 GMT) Full text and rfc822 format available.

Notification sent to Andreas Enge <andreas <at> enge.fr>:
bug acknowledged by developer. (Fri, 30 Jan 2015 16:08:03 GMT) Full text and rfc822 format available.

Message #19 received at 19708-done <at> debbugs.gnu.org (full text, mbox):

From: Mark H Weaver <mhw <at> netris.org>
To: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
Cc: Andreas Enge <andreas <at> enge.fr>, 19708-done <at> debbugs.gnu.org
Subject: Re: bug#19708: Bowtie fails to build
Date: Fri, 30 Jan 2015 11:07:51 -0500
Fixed in 241e12219.  Thanks to Ricardo and Andreas for sorting this out!

     Mark




bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Sat, 28 Feb 2015 12:24:03 GMT) Full text and rfc822 format available.

This bug report was last modified 10 years and 174 days ago.

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