Re: Fasta3 is non-free just because of some Smith Waterman implementation (Was: Please choose a free license for fasta3 components)
Hi Andreas,
Unfortunately I didn't get any answer, here is the mail I've sent to the
upstream.
https://lists.debian.org/debian-med/2019/09/msg00039.html
May be you or Steffen would like to try your luck, who knows, may be my
email went to spam or something like that.
Regards,
Alex
On 1/6/20 2:11 PM, Andreas Tille wrote:
> Hi again,
>
> any progress with this?
>
> Kind regards
>
> Andreas.
>
> On Fri, Sep 06, 2019 at 09:51:28AM +0200, Alex Mestiashvili wrote:
>> Thanks Erik!
>>
>> I'll try to get in touch with upstream and inform them that the code is
>> actually free.
>> However, while packaging of swsse2 makes sense, the source code is not
>> providing drop-in replacement for the code in fasta3. Nevertheless the
>> upstream of fasta3 can change the license anyway as far as I understand.
>>
>> Best,
>> Alex
>>
>>
>> On 9/6/19 9:22 AM, Andreas Tille wrote:
>>> Hi,
>>>
>>> beside the sad issue: Is someone taking over the packaging of the code
>>> and did you talked with fast3 upstream that the code is actually free?
>>>
>>> Kind regards
>>>
>>> Andreas.
>>>
>>> On Tue, Aug 20, 2019 at 02:39:05PM +0200, Steffen Möller wrote:
>>>> That is truly sad, indeed. Many thanks go to his widow and to Prof. Eddy
>>>> for caring. It is also an opportunity to think about how we as a
>>>> community can grow. A donation box for instance would never be enough to
>>>> feed the kids, but it would be something like a nice gesture about work
>>>> and his creator not being forgotten. We should possibly bring this up at
>>>> our next Sprint.
>>>>
>>>> Thank for this pointer, Erik.
>>>>
>>>> Steffen
>>>>
>>>> On 20.08.19 11:07, Erik Sjölund wrote:
>>>>> Hi Andreas,
>>>>>
>>>>> Regarding "Alex has once contacted upstream" note the sad news from
>>>>> https://cryptogenomicon.org/2019/03/11/farrars-striped-simd-smith-waterman/
>>>>>
>>>>> Kind regards,
>>>>> Erik
>>>>>
>>>>> On Mon, Aug 19, 2019 at 10:06 PM Andreas Tille <andreas@an3as.eu> wrote:
>>>>>> Hi Steffen,
>>>>>>
>>>>>> you have uploaded fasta3. When I wanted to upgrade to latest upstream I
>>>>>> realised that it is in non-free just because of two files implementing a
>>>>>> Smith Waterman algorithm. Alex has once contacted upstream as you can
>>>>>> see on our SoftwareLiberation page[1]. At least the wiki page does not
>>>>>> state any response.
>>>>>>
>>>>>> I wonder whether you might try to ping upstream or possibly use libssw
>>>>>> or libsmithwaterman as a replacement.
>>>>>>
>>>>>> Kind regards
>>>>>>
>>>>>> Andreas.
>>>>>>
>>>>>> [1] https://wiki.debian.org/DebianMed/SoftwareLiberation
>>>>>>
>>>>>> --
>>>>>> http://fam-tille.de
>>>>>>
>>>>
>>>>
>>>
>>
>>
>
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