From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH]: gnu: bowtie: only support x86_64-linux Date: Thu, 29 Jan 2015 12:16:47 +0100 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:37801) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YGn5o-0007Ws-5t for guix-devel@gnu.org; Thu, 29 Jan 2015 06:17:01 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1YGn5k-0007BB-Rv for guix-devel@gnu.org; Thu, 29 Jan 2015 06:17:00 -0500 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:56035) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1YGn5k-0007AJ-FA for guix-devel@gnu.org; Thu, 29 Jan 2015 06:16:56 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id B3DD02808BB for ; Thu, 29 Jan 2015 12:16:54 +0100 (CET) Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 8fXlO8VTKv5J for ; Thu, 29 Jan 2015 12:16:48 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Thu, 29 Jan 2015 12:16:47 +0100 (CET) In-Reply-To: List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel --=-=-= Content-Type: text/plain Ricardo Wurmus writes: > Since bowtie's Makefile explicitly checks that the system it is built on > is x86_64 building on MIPS and i686 should be disabled. (See bug#19708 > for discussion.) > > This is what the attached patch does. Please disregard the above patch and consider the attached one instead, which also patches the Makefile (with an upstream patch for the next release) to fix the build errors on x86_64. ~~ Ricardo --=-=-= Content-Type: text/x-patch; charset="utf-8" Content-Disposition: attachment; filename="0001-gnu-bowtie-fix-build-errors.patch" Content-Transfer-Encoding: quoted-printable >From cdabe548b67185e0c652ebacc90f95cfeffc5888 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 29 Jan 2015 10:35:52 +0100 Subject: [PATCH] gnu: bowtie: fix build errors * gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field= and add Makefile patch. * gnu/packages/patches/bowtie-fix-makefile.patch: New file. * gnu-system.am (MODULES): Add it. --- gnu-system.am | 1 + gnu/packages/bioinformatics.scm | 6 +++-- gnu/packages/patches/bowtie-fix-makefile.patch | 31 ++++++++++++++++++++= ++++++ 3 files changed, 36 insertions(+), 2 deletions(-) create mode 100644 gnu/packages/patches/bowtie-fix-makefile.patch diff --git a/gnu-system.am b/gnu-system.am index 6c2d66b..1211855 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -346,6 +346,7 @@ dist_patch_DATA =3D \ gnu/packages/patches/automake-skip-amhello-tests.patch \ gnu/packages/patches/avahi-localstatedir.patch \ gnu/packages/patches/avrdude-fix-libusb.patch \ + gnu/packages/patches/bowtie-fix-makefile.patch \ gnu/packages/patches/bigloo-gc-shebangs.patch \ gnu/packages/patches/binutils-ld-new-dtags.patch \ gnu/packages/patches/binutils-loongson-workaround.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm index ff6c337..620c809 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright =C2=A9 2014 Ricardo Wurmus +;;; Copyright =C2=A9 2014, 2015 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -95,7 +95,8 @@ BED, GFF/GTF, VCF.") (("^CPP =3D .*$") "CPP =3D g++") ;; replace BUILD_HOST and BUILD_TIME for deterministic= build (("-DBUILD_HOST=3D.*") "-DBUILD_HOST=3D\"\\\"guix\\\"\= "") - (("-DBUILD_TIME=3D.*") "-DBUILD_TIME=3D\"\\\"0\\\"\"")= )))) + (("-DBUILD_TIME=3D.*") "-DBUILD_TIME=3D\"\\\"0\\\"\"")= )) + (patches (list (search-patch "bowtie-fix-makefile.patch"))= ))) (build-system gnu-build-system) (inputs `(("perl" ,perl) ("perl-clone" ,perl-clone) @@ -133,6 +134,7 @@ aligning to relatively long (e.g. mammalian) genomes.= Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the huma= n genome, its memory footprint is typically around 3.2 GB. Bowtie 2 suppo= rts gapped, local, and paired-end alignment modes.") + (supported-systems '("x86_64-linux")) (license license:gpl3+))) =20 (define-public samtools diff --git a/gnu/packages/patches/bowtie-fix-makefile.patch b/gnu/package= s/patches/bowtie-fix-makefile.patch new file mode 100644 index 0000000..5ac6573 --- /dev/null +++ b/gnu/packages/patches/bowtie-fix-makefile.patch @@ -0,0 +1,31 @@ +From 4a99b0023bdfbbe486b9649489a32ea184c18c9a Mon Sep 17 00:00:00 2001 +From: Valentin Antonescu +Date: Tue, 2 Dec 2014 11:19:13 -0500 +Subject: [PATCH] Make sure the Mavericks test happens only under Darwin. + +--- + Makefile | 11 +++++------ + 1 file changed, 5 insertions(+), 6 deletions(-) + +diff --git a/Makefile b/Makefile +index d74f7c8..a4cdfa7 100644 +--- a/Makefile ++++ b/Makefile +@@ -54,12 +54,11 @@ endif + MACOS =3D 0 + ifneq (,$(findstring Darwin,$(shell uname))) + MACOS =3D 1 +-endif +- +-ifneq (,$(findstring 13,$(shell uname -r))) +- CPP =3D clang++ +- CC =3D clang +- EXTRA_FLAGS +=3D -stdlib=3Dlibstdc++ ++ ifneq (,$(findstring 13,$(shell uname -r))) ++ CPP =3D clang++ ++ CC =3D clang ++ EXTRA_FLAGS +=3D -stdlib=3Dlibstdc++ ++ endif + endif +=20 + POPCNT_CAPABILITY ?=3D 1 --=20 1.9.3 --=-=-=--