Re: Update mafft to 7.245.

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

On 17/12/15 22:47, Ricardo Wurmus wrote:
> Ben Woodcroft <b.woodcroft@uq.edu.au> 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