From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: Update mafft to 7.245. Date: Fri, 18 Dec 2015 06:01:59 +1000 Message-ID: <567314B7.7070605@uq.edu.au> References: <5641E082.90801@uq.edu.au> <20151110151207.6c5e4693@debian-netbook> <56426E2B.10405@uq.edu.au> <567001F0.7060206@uq.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:36314) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a9ekj-00011K-PH for guix-devel@gnu.org; Thu, 17 Dec 2015 15:02:18 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a9ekf-0000aT-G8 for guix-devel@gnu.org; Thu, 17 Dec 2015 15:02:17 -0500 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:52128 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a9eke-0000Yh-UM for guix-devel@gnu.org; Thu, 17 Dec 2015 15:02:13 -0500 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: Ricardo Wurmus Cc: "guix-devel@gnu.org" On 17/12/15 22:47, Ricardo Wurmus wrote: > Ben Woodcroft writes: > >>> What do you think? >> I think you are quite valiant. As I say, I cannot be confident in my >> testing (even those in the readme). The diff looked mostly fine by eye= , >> but there was some issues near the end which mangled things somewhat > What was mangled? Original: tmpawk=3D`which nawk 2>/dev/null | awk '{print $1}'` if [ -x "$tmpawk" ]; then prog=3D"$tmpawk" fi tmpawk=3D`which gawk 2>/dev/null | awk '{print $1}'` if [ -x "$tmpawk" ]; then prog=3D"$tmpawk" fi After your patch: tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk=3D`whic= h=20 n/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk=20 2>/dev/null | /gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/= aw if [ -x=20 "$tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk" ]; t= hen prog=3D"$tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/aw= k" fi tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk=3D`whic= h=20 g/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk=20 2>/dev/null | /gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/= aw if [ -x=20 "$tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk" ]; t= hen prog=3D"$tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/aw= k" fi The most recent patch: tmpawk=3D`which nawk 2>/dev/null |=20 /gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk '{print $1= }'` if [ -x "$tmpawk" ]; then prog=3D"$tmpawk" fi tmpawk=3D`which gawk 2>/dev/null |=20 /gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk '{print $1= }'` if [ -x "$tmpawk" ]; then prog=3D"$tmpawk" fi > >> (although maybe not the result, not sure). How's the attached? I upped >> version too. OK? > I think this line may be problematic: > >> + (("([\"`| ])awk" _ prefix) > Is your intent really to replace =E2=80=9C awk=E2=80=9D and =E2=80=9C|a= wk=E2=80=9D? Yes, is that not a good idea? > In my previous > patch I tried to more explicit by using alternatives in the group: > >> + (("(\"|`|\| )awk" _ prefix) > Was there a problem with the version above? It does not replace =E2=80= =9C awk=E2=80=9D > and =E2=80=9C|awk=E2=80=9D but only =E2=80=9C| awk=E2=80=9D (in additio= n to the other two variants). OK. Seems something went astray though. > Other than that the patch does look fine. If you confirm that this is > what you intended then I=E2=80=99ll push it as is. Thanks, if you are happy. This was just supposed to be a simple update.. I tried adding a check procedure but this didn't work: mafft refused to=20 run, when it runs just fine from the store. I was loath to debug that.=20 Instead, I was wondering if there was a way to test after installation?=20 If these tests could be run in a container that excluded native-inputs=20 (but perhaps some extra test-specific dependencies if required), then I=20 think such a procedure could be generally quite useful. It would catch=20 the errors I made in the original patch, for instance. Thank you. ben