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Re: Update mafft to 7.245.


From: Ben Woodcroft
Subject: Re: Update mafft to 7.245.
Date: Fri, 18 Dec 2015 06:01:59 +1000
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Thunderbird/38.4.0



On 17/12/15 22:47, Ricardo Wurmus wrote:
Ben Woodcroft <address@hidden> 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=`which nawk 2>/dev/null | awk '{print $1}'`
if [ -x "$tmpawk" ]; then
        prog="$tmpawk"
fi

tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
if [ -x "$tmpawk" ]; then
        prog="$tmpawk"
fi


After your patch:

tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk=`which n/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk 2>/dev/null | /gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/aw if [ -x "$tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk" ]; then
prog="$tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk"
fi

tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk=`which g/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk 2>/dev/null | /gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/aw if [ -x "$tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk" ]; then
prog="$tmp/gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk"
fi


The most recent patch:

tmpawk=`which nawk 2>/dev/null | /gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk '{print $1}'`
if [ -x "$tmpawk" ]; then
        prog="$tmpawk"
fi

tmpawk=`which gawk 2>/dev/null | /gnu/store/k8qgvgwn5anbfy8r70h938kxgd46cyxx-gawk-4.1.3/bin/awk '{print $1}'`
if [ -x "$tmpawk" ]; then
        prog="$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 “ awk” and “|awk”?
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 “ awk”
and “|awk” but only “| awk” (in addition 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’ll 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 run, when it runs just fine from the store. I was loath to debug that. Instead, I was wondering if there was a way to test after installation? If these tests could be run in a container that excluded native-inputs (but perhaps some extra test-specific dependencies if required), then I think such a procedure could be generally quite useful. It would catch the errors I made in the original patch, for instance.

Thank you.
ben



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