From unknown Tue Aug 19 05:28:44 2025 X-Loop: help-debbugs@gnu.org Subject: bug#19708: Bowtie fails to build Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Tue, 27 Jan 2015 21:48:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 19708 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 19708@debbugs.gnu.org X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.142239526712479 (code B ref -1); Tue, 27 Jan 2015 21:48:01 +0000 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 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-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 unknown Tue Aug 19 05:28:44 2025 X-Loop: help-debbugs@gnu.org Subject: bug#19708: Bowtie fails to build Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Wed, 28 Jan 2015 14:12:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 19708 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Andreas Enge Cc: 19708@debbugs.gnu.org Received: via spool by 19708-submit@debbugs.gnu.org id=B19708.142245428219227 (code B ref 19708); Wed, 28 Jan 2015 14:12:01 +0000 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 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-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 unknown Tue Aug 19 05:28:44 2025 X-Loop: help-debbugs@gnu.org Subject: bug#19708: Bowtie fails to build Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Wed, 28 Jan 2015 16:58:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 19708 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 19708@debbugs.gnu.org Received: via spool by 19708-submit@debbugs.gnu.org id=B19708.14224642682861 (code B ref 19708); Wed, 28 Jan 2015 16:58:03 +0000 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 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-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 unknown Tue Aug 19 05:28:44 2025 X-Loop: help-debbugs@gnu.org Subject: bug#19708: Bowtie fails to build Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Thu, 29 Jan 2015 10:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 19708 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Andreas Enge Cc: 19708@debbugs.gnu.org Received: via spool by 19708-submit@debbugs.gnu.org id=B19708.142252573622983 (code B ref 19708); Thu, 29 Jan 2015 10:03:02 +0000 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 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-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 unknown Tue Aug 19 05:28:44 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.503 (Entity 5.503) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Andreas Enge Subject: bug#19708: closed (Re: bug#19708: Bowtie fails to build) Message-ID: References: <87d25wp7zc.fsf@netris.org> <20150127214727.GA6287@debian> X-Gnu-PR-Message: they-closed 19708 X-Gnu-PR-Package: guix Reply-To: 19708@debbugs.gnu.org Date: Fri, 30 Jan 2015 16:08:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1422634083-25771-1" This is a multi-part message in MIME format... ------------=_1422634083-25771-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #19708: Bowtie fails to build which was filed against the guix package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 19708@debbugs.gnu.org. --=20 19708: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D19708 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1422634083-25771-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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 ------------=_1422634083-25771-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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 ------------=_1422634083-25771-1--