From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 27 16:47:47 2015 Received: (at submit) by debbugs.gnu.org; 27 Jan 2015 21:47:47 +0000 Received: from localhost ([127.0.0.1]:58352 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YGDz9-0003FC-9h for submit@debbugs.gnu.org; Tue, 27 Jan 2015 16:47:47 -0500 Received: from eggs.gnu.org ([208.118.235.92]:35502) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YGDz6-0003Ey-U7 for submit@debbugs.gnu.org; Tue, 27 Jan 2015 16:47:45 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YGDz0-0003Oa-6C for submit@debbugs.gnu.org; Tue, 27 Jan 2015 16:47:39 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:40858) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YGDz0-0003OU-3r for submit@debbugs.gnu.org; Tue, 27 Jan 2015 16:47:38 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:37219) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YGDyz-00010Y-5w for bug-guix@gnu.org; Tue, 27 Jan 2015 16:47:38 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YGDyv-0003H1-VF for bug-guix@gnu.org; Tue, 27 Jan 2015 16:47:37 -0500 Received: from mout.kundenserver.de ([212.227.17.10]:49662) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YGDyv-0003Go-Mb for bug-guix@gnu.org; Tue, 27 Jan 2015 16:47:33 -0500 Received: from debian ([82.66.2.95]) by mrelayeu.kundenserver.de (mreue104) with ESMTPSA (Nemesis) id 0Lmufk-1XkUCD2uJo-00h49Y; Tue, 27 Jan 2015 22:47:29 +0100 Date: Tue, 27 Jan 2015 22:47:27 +0100 From: Andreas Enge To: bug-guix@gnu.org Subject: Bowtie fails to build Message-ID: <20150127214727.GA6287@debian> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.23 (2014-03-12) X-Provags-ID: V03:K0:GYfX4AAcDY9T98QSlSomB1t4b7ewv/cyd0vHEUvoLzVVIw++jPW Cp5/vKZ0bviyMwM0Waz2q6hts72wtmnx3zO+h0fDv+9kTZsLn2tnJTWgpR7LMXhuk6qb0S+ k3M794zsV58e1rjqk4rdjGifkK5tEiPvtI6/anX/rHU/5hURtuFBvHc72tEIuyIG0HKWPBj ud2ZqF/KoA3UZJCrPd1ng== X-UI-Out-Filterresults: notjunk:1; X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [generic] X-detected-operating-system: by eggs.gnu.org: Error: Malformed IPv6 address (bad octet value). X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) 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 From debbugs-submit-bounces@debbugs.gnu.org Wed Jan 28 09:11:22 2015 Received: (at 19708) by debbugs.gnu.org; 28 Jan 2015 14:11:22 +0000 Received: from localhost ([127.0.0.1]:58603 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YGTL0-000503-52 for submit@debbugs.gnu.org; Wed, 28 Jan 2015 09:11:22 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:46589) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YGTKx-0004zn-GG for 19708@debbugs.gnu.org; Wed, 28 Jan 2015 09:11:20 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id BEA54380665; Wed, 28 Jan 2015 15:11:13 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:references:received :received:received; s=mdc; t=1422454268; x=1424268669; bh=CNBlFw cpeeNcT7Oyl+MlKuvZEAJSxvdkYtNrO93ta+w=; b=McKZL9TQFp1PnrW7n7JEt3 RoqXjCK36Ld6AltHP8jJe9AX8AYfIKHGz5pC480NOPAdipH6foQ/VLs1M+1AoaFW nAPeh4BtOSUf+uztX6baiLLo0Y28D8bKI19eJ42O8wB81fIxjtuyqCqDz7lE4nic IL9AsfBICGnar+ltWvPs4= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id b_QBKeNzpZqd; Wed, 28 Jan 2015 15:11:08 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP; Wed, 28 Jan 2015 15:11:08 +0100 (CET) Received: from localhost (141.80.180.135) by HTCATWO.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.210.2; Wed, 28 Jan 2015 15:11:07 +0100 References: <20150127214727.GA6287@debian> From: Ricardo Wurmus To: Andreas Enge Subject: Re: bug#19708: Bowtie fails to build In-Reply-To: <20150127214727.GA6287@debian> Date: Wed, 28 Jan 2015 15:11:06 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-10.0.0.4211-7.500.1017-21288.007 X-TM-AS-Result: No--0.179500-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 19708 Cc: 19708@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) 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 From debbugs-submit-bounces@debbugs.gnu.org Wed Jan 28 11:57:48 2015 Received: (at 19708) by debbugs.gnu.org; 28 Jan 2015 16:57:48 +0000 Received: from localhost ([127.0.0.1]:59170 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YGVw3-0000k3-Fj for submit@debbugs.gnu.org; Wed, 28 Jan 2015 11:57:47 -0500 Received: from mout.kundenserver.de ([212.227.17.13]:57590) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YGVw1-0000jc-HZ for 19708@debbugs.gnu.org; Wed, 28 Jan 2015 11:57:46 -0500 Received: from debian.math.u-bordeaux1.fr ([147.210.21.57]) by mrelayeu.kundenserver.de (mreue104) with ESMTPSA (Nemesis) id 0M25kJ-1XO0dc0V9X-00u3FC; Wed, 28 Jan 2015 17:57:39 +0100 Date: Wed, 28 Jan 2015 17:57:35 +0100 From: Andreas Enge To: Ricardo Wurmus Subject: Re: bug#19708: Bowtie fails to build Message-ID: <20150128165735.GA14986@debian.math.u-bordeaux1.fr> References: <20150127214727.GA6287@debian> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.5.23 (2014-03-12) X-Provags-ID: V03:K0:hYd4dpLkxzFsSbLOznX3lI1Q8Vndi7XFVPkC8OPyODMAD5MKyEV Astk6tp+F/DMYZHlyWoan0HK8iJl37k1O3/UMWhB7bkm050tw1xxv5FwAqPW+jjxQBiUbgb FBLOFAj1gkULPtW51o0Y6Sk8kJRV1lNTjya8+Yc/eHWaXNLf4VX8BoK5QhdNP2VmoRy2OyB eWKO3q88Qxy+ORhyTaTyQ== X-UI-Out-Filterresults: notjunk:1; X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 19708 Cc: 19708@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 0.0 (/) 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 From debbugs-submit-bounces@debbugs.gnu.org Thu Jan 29 05:02:16 2015 Received: (at 19708) by debbugs.gnu.org; 29 Jan 2015 10:02:16 +0000 Received: from localhost ([127.0.0.1]:56831 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YGlvU-0005yd-0B for submit@debbugs.gnu.org; Thu, 29 Jan 2015 05:02:16 -0500 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:50096) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YGlvQ-0005yM-1h for 19708@debbugs.gnu.org; Thu, 29 Jan 2015 05:02:13 -0500 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 2F6293805A2; Thu, 29 Jan 2015 11:02:06 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:references:received :received:received; s=mdc; t=1422525720; x=1424340121; bh=9GNzVF bc/4m8F3Ztg1Ikv95tloaHmwCQ67Ry7Nsg+6A=; b=qrH/DTYSKRNzf8dLdVT16z c1Io+0oi3ApfAF/6CRS7Oh6Fsibp82MTvtHjzW4eaGVfQ2bSGbRv/S/hgYhLy7+/ bJSf/PjLKn3vHeNj4rPNuOdDVD5bNnB2CnQwIrmDVINIK3CbOSqS+O350KEz2Ajr /NhOENEew6M0bh2Qif4oo= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id Ocuo_Ae9qEc9; Thu, 29 Jan 2015 11:02:00 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP; Thu, 29 Jan 2015 11:02:00 +0100 (CET) Received: from localhost (141.80.180.135) by HTCATWO.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.210.2; Thu, 29 Jan 2015 11:01:56 +0100 References: <20150127214727.GA6287@debian> <20150128165735.GA14986@debian.math.u-bordeaux1.fr> From: Ricardo Wurmus To: Andreas Enge Subject: Re: bug#19708: Bowtie fails to build In-Reply-To: <20150128165735.GA14986@debian.math.u-bordeaux1.fr> Date: Thu, 29 Jan 2015 11:01:56 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-10.0.0.4211-7.500.1017-21290.006 X-TM-AS-Result: No--3.916700-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 19708 Cc: 19708@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) 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 From debbugs-submit-bounces@debbugs.gnu.org Fri Jan 30 11:07:57 2015 Received: (at 19708-done) by debbugs.gnu.org; 30 Jan 2015 16:07:57 +0000 Received: from localhost ([127.0.0.1]:58227 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YHE6v-0006hG-BB for submit@debbugs.gnu.org; Fri, 30 Jan 2015 11:07:57 -0500 Received: from world.peace.net ([50.252.239.5]:60665 ident=hope2) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1YHE6t-0006h8-CE for 19708-done@debbugs.gnu.org; Fri, 30 Jan 2015 11:07:55 -0500 Received: from [10.1.10.12] (helo=jojen) by world.peace.net with esmtpsa (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.72) (envelope-from ) id 1YHE6k-0001H1-85; Fri, 30 Jan 2015 11:07:46 -0500 From: Mark H Weaver To: Ricardo Wurmus Subject: Re: bug#19708: Bowtie fails to build References: <20150127214727.GA6287@debian> <20150128165735.GA14986@debian.math.u-bordeaux1.fr> Date: Fri, 30 Jan 2015 11:07:51 -0500 In-Reply-To: (Ricardo Wurmus's message of "Thu, 29 Jan 2015 11:01:56 +0100") Message-ID: <87d25wp7zc.fsf@netris.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/24.4 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 19708-done Cc: Andreas Enge , 19708-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 0.0 (/) Fixed in 241e12219. Thanks to Ricardo and Andreas for sorting this out! Mark From unknown Tue Aug 19 05:26:25 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sat, 28 Feb 2015 12:24:03 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator