Ok, I understand what was my problem. In the `bin/` folder I had a
directory named `tmp`. This was collapsing with target that was trying
to create a tmp file with name `tmp`. Since I had the directory, make
was not happy. I don't know where the `tmp` folder was coming from
tough.

I attached a patch that now use a more specific tmp file instead of
`tmp`. Feel free to include it or not since there is no real bug in
the Makefile.

Regards,
Matt

On Fri, Sep 20, 2013 at 3:53 PM, Per Bothner <per@bothner.com> wrote:
> On 09/20/2013 11:51 AM, Matthieu Vachon wrote:
>>
>> When arriving at this Makefile, the build failed saying that `tmp` is
>> a folder and cannot be written to. This problem comes from this line
>> in the Makefile (there is more that one instance):
>>
>>      echo '#!/bin/sh' >tmp
>> ...
>>
>> What would be the right fix for this problem?
>
>
> The testsuite mostly uses names that *start* with tmp,
> such as tmp.out or tmp-knucleotide1.log.
>
> Using the tmp.xxx form is compatible with the mktemp
> command, but it is conceivable some filesystems (like FAT)
> would have problems (but they would probably have problems
> regardless), so perhaps the tmp-xxx form is preferable.
>
> So for gckawa instead of tmp maybe use tmp-gckawa.
>
> The CLEANFILES macro would need to be updated,
> presumably to tmp-*.
> --
>         --Per Bothner
> per@bothner.com   http://per.bothner.com/