From patchwork Wed Nov 7 19:56:53 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Christopher Baines X-Patchwork-Id: 142 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id A60B9167CF; Wed, 7 Nov 2018 19:57:25 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, UNPARSEABLE_RELAY,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id 5D0EE167CD for ; Wed, 7 Nov 2018 19:57:25 +0000 (GMT) Received: from localhost ([::1]:50963 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gKTx6-0002qa-K7 for patchwork@mira.cbaines.net; Wed, 07 Nov 2018 14:57:24 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:48830) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gKTx0-0002q5-0k for guix-patches@gnu.org; Wed, 07 Nov 2018 14:57:21 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gKTwm-0002pe-SU for guix-patches@gnu.org; Wed, 07 Nov 2018 14:57:12 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:35669) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gKTwk-0002om-DU for guix-patches@gnu.org; Wed, 07 Nov 2018 14:57:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gKTwk-0002cn-By for guix-patches@gnu.org; Wed, 07 Nov 2018 14:57:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33308] [PATCH 1/2] gnu: mash: Update to 2.1. References: <87va58hdt1.fsf@cbaines.net> In-Reply-To: <87va58hdt1.fsf@cbaines.net> Resent-From: Christopher Baines Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 07 Nov 2018 19:57:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33308 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 33308@debbugs.gnu.org Received: via spool by 33308-submit@debbugs.gnu.org id=B33308.154162062110075 (code B ref 33308); Wed, 07 Nov 2018 19:57:02 +0000 Received: (at 33308) by debbugs.gnu.org; 7 Nov 2018 19:57:01 +0000 Received: from localhost ([127.0.0.1]:39926 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gKTwi-0002cR-Ob for submit@debbugs.gnu.org; Wed, 07 Nov 2018 14:57:00 -0500 Received: from li622-129.members.linode.com ([212.71.249.129]:55916 helo=mira.cbaines.net) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gKTwg-0002cB-8J for 33308@debbugs.gnu.org; Wed, 07 Nov 2018 14:56:58 -0500 Received: by mira.cbaines.net (Postfix, from userid 113) id C4941167CF; Wed, 7 Nov 2018 19:56:57 +0000 (GMT) Received: from localhost (cpc102582-walt20-2-0-cust14.13-2.cable.virginm.net [86.27.34.15]) by mira.cbaines.net (Postfix) with ESMTPSA id E8F31167CD for <33308@debbugs.gnu.org>; Wed, 7 Nov 2018 19:56:54 +0000 (GMT) Received: from localhost (localhost [local]) by localhost (OpenSMTPD) with ESMTPA id fd886518 for <33308@debbugs.gnu.org>; Wed, 7 Nov 2018 19:56:54 +0000 (UTC) From: Christopher Baines Date: Wed, 7 Nov 2018 19:56:53 +0000 Message-Id: <20181107195654.22832-1-mail@cbaines.net> X-Mailer: git-send-email 2.19.1 MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore, update it, and tweak the compilation to allow it to build with 0.7. The package also builds with the current version of capnproto. I got the idea of changing the c++ version from here [1]. 1: https://github.com/marbl/Mash/issues/98 * gnu/packages/bioinformatics.scm (mash)[version]: Change to 2.1. [source]: Update sha256 hash. [arguments]: Add new use-c++14 phase, to patch source to build using c++14. --- gnu/packages/bioinformatics.scm | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9f0b8025da..93503d82b8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3977,7 +3977,7 @@ sequences).") (define-public mash (package (name "mash") - (version "2.0") + (version "2.1") (source (origin (method url-fetch) (uri (string-append @@ -3986,7 +3986,7 @@ sequences).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv")) + "0d5m9wx1bspa5vwikazdbar4i0h6b20lzjjl1icfyl66sy1q9v9q")) (modules '((guix build utils))) (snippet '(begin @@ -4012,7 +4012,15 @@ sequences).") (("^#include \"kseq\\.h\"") "#include \"htslib/kseq.h\"")) #t)) - (add-after 'fix-includes 'autoconf + (add-after 'fix-includes 'use-c++14 + (lambda _ + ;; capnproto 0.7 requires c++14 to build + (substitute* "configure.ac" + (("c\\+\\+11") "c++14")) + (substitute* "Makefile.in" + (("c\\+\\+11") "c++14")) + #t)) + (add-after 'use-c++14 'autoconf (lambda _ (zero? (system* "autoconf"))))))) (native-inputs `(("autoconf" ,autoconf) From patchwork Mon Nov 26 19:04:33 2018 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Christopher Baines X-Patchwork-Id: 319 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 8A30216826; Mon, 26 Nov 2018 19:05:17 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.9 required=5.0 tests=BAYES_00,RCVD_IN_DNSWL_HI, UNPARSEABLE_RELAY,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:4830:134:3::11]) by mira.cbaines.net (Postfix) with ESMTPS id 2A4831681B for ; Mon, 26 Nov 2018 19:05:17 +0000 (GMT) Received: from localhost ([::1]:38263 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gRMC4-000846-5H for patchwork@mira.cbaines.net; Mon, 26 Nov 2018 14:05:16 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:58036) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gRMBx-00083v-9s for guix-patches@gnu.org; Mon, 26 Nov 2018 14:05:10 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gRMBq-0008Qu-OY for guix-patches@gnu.org; Mon, 26 Nov 2018 14:05:09 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:45857) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gRMBq-0008Qp-Lc for guix-patches@gnu.org; Mon, 26 Nov 2018 14:05:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gRMBq-0007Jl-CM for guix-patches@gnu.org; Mon, 26 Nov 2018 14:05:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#33308] [PATCH v2 2/2] gnu: capnproto: Update to 0.7.0. Resent-From: Christopher Baines Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 26 Nov 2018 19:05:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33308 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 33308@debbugs.gnu.org Received: via spool by 33308-submit@debbugs.gnu.org id=B33308.154325907728083 (code B ref 33308); Mon, 26 Nov 2018 19:05:02 +0000 Received: (at 33308) by debbugs.gnu.org; 26 Nov 2018 19:04:37 +0000 Received: from localhost ([127.0.0.1]:50112 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gRMBR-0007It-37 for submit@debbugs.gnu.org; Mon, 26 Nov 2018 14:04:37 -0500 Received: from li622-129.members.linode.com ([212.71.249.129]:49708 helo=mira.cbaines.net) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gRMBP-0007Ik-8x for 33308@debbugs.gnu.org; Mon, 26 Nov 2018 14:04:36 -0500 Received: by mira.cbaines.net (Postfix, from userid 113) id 44D2816862; Mon, 26 Nov 2018 19:04:34 +0000 (GMT) Received: from localhost (cpc102582-walt20-2-0-cust14.13-2.cable.virginm.net [86.27.34.15]) by mira.cbaines.net (Postfix) with ESMTPSA id DC6F71681F for <33308@debbugs.gnu.org>; Mon, 26 Nov 2018 19:04:33 +0000 (GMT) Received: from localhost (localhost [local]) by localhost (OpenSMTPD) with ESMTPA id 959d100c for <33308@debbugs.gnu.org>; Mon, 26 Nov 2018 19:04:33 +0000 (UTC) From: Christopher Baines Date: Mon, 26 Nov 2018 19:04:33 +0000 Message-Id: <20181126190433.25295-2-mail@cbaines.net> X-Mailer: git-send-email 2.19.2 In-Reply-To: <20181126190433.25295-1-mail@cbaines.net> References: <87va58hdt1.fsf@cbaines.net> <20181126190433.25295-1-mail@cbaines.net> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 208.118.235.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/serialization.scm (capnproto): Update to 0.7.0. [arguments]: Add new 'use-tmp-for-tempory-files phase. --- gnu/packages/serialization.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 2df0ce1364..2d61f7451b 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -306,7 +306,7 @@ it a convenient format to store user input files.") (define-public capnproto (package (name "capnproto") - (version "0.6.1") + (version "0.7.0") (source (origin (method url-fetch) (uri (string-append @@ -314,7 +314,7 @@ it a convenient format to store user input files.") version ".tar.gz")) (sha256 (base32 - "010s9yhq4531wvdfrdf2477zswhck6cjfby79w73rff3v06090l0")))) + "0hfdnhlbskagzgvby8wy6lrxj53zfzpfqimbhga68c0ji2yw1969")))) (build-system gnu-build-system) (arguments `(#:phases @@ -324,6 +324,14 @@ it a convenient format to store user input files.") ;; Workaround for test that tries to resolve port name from ;; /etc/services, which is not present in build environment. (substitute* "src/kj/async-io-test.c++" ((":http") ":80")) + #t)) + (add-before 'check 'use-tmp-for-tempory-files + (lambda _ + ;; Use /tmp for tempory files, as the default /var/tmp directory + ;; doesn't exist. + (substitute* "src/kj/filesystem-disk-test.c++" + (("VAR\\_TMP \"/var/tmp\"") + "VAR_TMP \"/tmp\"")) #t))))) (home-page "https://capnproto.org") (synopsis "Capability-based RPC and serialization system")