RFS paml - fixed #957659

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RFS paml - fixed #957659

Étienne Mollier
Good day,

I fixed another Gcc-10 FTBFS, for the "paml" package this time,
and took this opportunity to run routine-update.  Manual pages
are still missing though.  Actually, I have no clue how are
supposed to be used these programs, so it may be better if
someone having little background in phylogenic analysis has a
look at this.

I have not forwarded the patch for the moment, since reporting
bugs requires posting in a Google Group that forbids contact
through email, and I have no Google account for the moment, at
least none usable to my knowledge.  :(

Kind Regards,
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Re: RFS paml - fixed #957659

Andreas Tille-5
Hi Étienne,

On Fri, May 08, 2020 at 02:27:37PM +0200, Étienne Mollier wrote:
> I fixed another Gcc-10 FTBFS, for the "paml" package this time,
> and took this opportunity to run routine-update.

Thanks a lot.

> Manual pages
> are still missing though.  Actually, I have no clue how are
> supposed to be used these programs, so it may be better if
> someone having little background in phylogenic analysis has a
> look at this.

I tend to use help2man but as you might have noticed this does
not work here.

> I have not forwarded the patch for the moment, since reporting
> bugs requires posting in a Google Group that forbids contact
> through email, and I have no Google account for the moment, at
> least none usable to my knowledge.  :(

IMHO if upstream makes it very hard to be contacted our effort
we should do should not be exagerated.

Kind regards

      Andreas.

--
http://fam-tille.de

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Re: RFS paml - fixed #957659

Étienne Mollier
Hi Andreas,

Andreas Tille, on 2020-05-09 15:01:33 +0200:
> On Fri, May 08, 2020 at 02:27:37PM +0200, Étienne Mollier wrote:
> > I fixed another Gcc-10 FTBFS, for the "paml" package this time,
> > and took this opportunity to run routine-update.
>
> Thanks a lot.

You're welcome, thanks for the upload.

> > I have not forwarded the patch for the moment, since reporting
> > bugs requires posting in a Google Group that forbids contact
> > through email, and I have no Google account for the moment, at
> > least none usable to my knowledge.  :(
>
> IMHO if upstream makes it very hard to be contacted our effort
> we should do should not be exagerated.

I'm not entirely sure I understood your opinion, but if there
are more projects requiring a Google Account to contact
upstream, then I'll probably reconsider getting one.

After all, there are so many projects on Github today, that I
ended up opening an account last month just to allow myself
interacting with upstream.  It seems to have been a good move
given the positive reactions I received on that side so far.  :)

Kind Regards,
--
Étienne Mollier <[hidden email]>
Fingerprint:  5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
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Re: RFS paml - fixed #957659

Andreas Tille-5
On Sat, May 09, 2020 at 04:35:16PM +0200, Étienne Mollier wrote:
> > IMHO if upstream makes it very hard to be contacted our effort
> > we should do should not be exagerated.
>
> I'm not entirely sure I understood your opinion, but if there
> are more projects requiring a Google Account to contact
> upstream, then I'll probably reconsider getting one.

I intended to say that upstream should not require people to
create any account if they are interested in feedback.
 
> After all, there are so many projects on Github today, that I
> ended up opening an account last month just to allow myself
> interacting with upstream.  It seems to have been a good move
> given the positive reactions I received on that side so far.  :)

Github is quite an important development platform and our BTS is
checking Github issues if the forward property is set accordingly.  Here
it makes more sense than subscribing a Google list which will spam you
with noise.

Kind regards

      Andreas.

--
http://fam-tille.de

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Re: RFS paml - fixed #957659

Étienne Mollier
Hi Andreas,

Andreas Tille, on 2020-05-09 18:44:40 +0200:

> On Sat, May 09, 2020 at 04:35:16PM +0200, Étienne Mollier wrote:
> > > IMHO if upstream makes it very hard to be contacted our effort
> > > we should do should not be exagerated.
> >
> > I'm not entirely sure I understood your opinion, but if there
> > are more projects requiring a Google Account to contact
> > upstream, then I'll probably reconsider getting one.
>
> I intended to say that upstream should not require people to
> create any account if they are interested in feedback.
>  
> > After all, there are so many projects on Github today, that I
> > ended up opening an account last month just to allow myself
> > interacting with upstream.  It seems to have been a good move
> > given the positive reactions I received on that side so far.  :)
>
> Github is quite an important development platform and our BTS is
> checking Github issues if the forward property is set accordingly.  Here
> it makes more sense than subscribing a Google list which will spam you
> with noise.
Thank you for your clarification, and the warning about Google
lists.  It is unfortunate but sound ; and I guess if upstream
wishes to not be contacted in conventional way, this should be
respected as well.

So it looks like the situation is fair enough as is I guess.
Kind Regards,
--
Étienne Mollier <[hidden email]>
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Re: RFS paml - fixed #957659

Michael Crusoe
In reply to this post by Étienne Mollier


On Fri, May 8, 2020 at 2:27 PM Étienne Mollier <[hidden email]> wrote:
Good day,


I have not forwarded the patch for the moment, since reporting
bugs requires posting in a Google Group that forbids contact
through email, and I have no Google account for the moment, at
least none usable to my knowledge.  :(

Feel free to use me as a mail forwarder :-)


--
Michael R. Crusoe
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Re: RFS paml - fixed #957659

Étienne Mollier
Hi Michael,

Michael Crusoe, on 2020-05-09 19:48:06 +0200:

> On Fri, May 8, 2020 at 2:27 PM Étienne Mollier <[hidden email]>
> wrote:
>
> > Good day,
> >
> >
> > I have not forwarded the patch for the moment, since reporting
> > bugs requires posting in a Google Group that forbids contact
> > through email, and I have no Google account for the moment, at
> > least none usable to my knowledge.  :(
> >
>
> Feel free to use me as a mail forwarder :-)
Good point!  That's one of the good things about being part of a
team of course!  :)

Please, if you, or anyone else in the team having a Google
account, would be kind enough to forward the patch against
src/paml.h fixing #957659[0], available both here[1] and in
attachment, and which follows GNU recommendation toward using
"extern" statements for globals in use in multiple files when
moving to Gcc 10[2], to the Google Group related to the PAML
software[3], then that would be really nice.  :)

[0] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957659
[1] https://salsa.debian.org/med-team/paml/-/blob/master/debian/patches/gcc10.patch
[2] https://gcc.gnu.org/gcc-10/porting_to.html
[3] https://groups.google.com/forum/#!forum/pamlsoftware

Kind Regards,
--
Étienne Mollier <[hidden email]>
Fingerprint:  5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
Help find cures against the Covid-19 !  Give CPU cycles:
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Re: RFS paml - fixed #957659

Julien Yann Dutheil-2
Hi,

For once, maybe I can be of some help there. I shall be able to reach the author of PAML directly... shall I give it a try?

Julien.

On Sat, May 9, 2020 at 8:31 PM Étienne Mollier <[hidden email]> wrote:
Hi Michael,

Michael Crusoe, on 2020-05-09 19:48:06 +0200:
> On Fri, May 8, 2020 at 2:27 PM Étienne Mollier <[hidden email]>
> wrote:
>
> > Good day,
> >
> >
> > I have not forwarded the patch for the moment, since reporting
> > bugs requires posting in a Google Group that forbids contact
> > through email, and I have no Google account for the moment, at
> > least none usable to my knowledge.  :(
> >
>
> Feel free to use me as a mail forwarder :-)

Good point!  That's one of the good things about being part of a
team of course!  :)

Please, if you, or anyone else in the team having a Google
account, would be kind enough to forward the patch against
src/paml.h fixing #957659[0], available both here[1] and in
attachment, and which follows GNU recommendation toward using
"extern" statements for globals in use in multiple files when
moving to Gcc 10[2], to the Google Group related to the PAML
software[3], then that would be really nice.  :)

[0] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957659
[1] https://salsa.debian.org/med-team/paml/-/blob/master/debian/patches/gcc10.patch
[2] https://gcc.gnu.org/gcc-10/porting_to.html
[3] https://groups.google.com/forum/#!forum/pamlsoftware

Kind Regards,
--
Étienne Mollier <[hidden email]>
Fingerprint:  5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
Help find cures against the Covid-19 !  Give CPU cycles:
  * Rosetta@home: https://boinc.bakerlab.org/rosetta/
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--
Julien Y. Dutheil, Ph-D
0 (+49) 4522 763 298

§ Max Planck Institute for Evolutionary Biology
Molecular Systems Evolution
Department of Evolutionary Genetics
Plön -- GERMANY

§ Institute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE
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Re: RFS paml - fixed #957659

Andreas Tille-5
On Sat, May 09, 2020 at 10:32:32PM +0200, Julien Yann Dutheil wrote:
> For once, maybe I can be of some help there. I shall be able to reach the
> author of PAML directly... shall I give it a try?

Yes, please forward the patch - basically in the interest of the PAML
authors themselves.

Kind regards

     Andreas.

--
http://fam-tille.de

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Re: RFS paml - fixed #957659

Étienne Mollier
Hi Julien,

Andreas Tille, on 2020-05-10 07:06:09 +0200:
> On Sat, May 09, 2020 at 10:32:32PM +0200, Julien Yann Dutheil wrote:
> > For once, maybe I can be of some help there. I shall be able to reach the
> > author of PAML directly... shall I give it a try?
>
> Yes, please forward the patch - basically in the interest of the PAML
> authors themselves.

Sure!  In case you're afraid of colliding with Michael or
someone else, it's better to have a duplicate entry in a bug
tracker, and mark is as such, than no entry at all.  :)

Kind Regards,
--
Étienne Mollier <[hidden email]>
Fingerprint:  5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
Help find cures against the Covid-19 !  Give CPU cycles:
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Re: RFS paml - fixed #957659

Julien Yann Dutheil-2
Hi,

Got a reply from Ziheng Yang, the author of PAML. He said he will include the suggested changes upstream.

Best,

Julien.

PS: does this solve the issue or is there anything else I should do :s ?

On Sun, May 10, 2020 at 11:59 AM Étienne Mollier <[hidden email]> wrote:
Hi Julien,

Andreas Tille, on 2020-05-10 07:06:09 +0200:
> On Sat, May 09, 2020 at 10:32:32PM +0200, Julien Yann Dutheil wrote:
> > For once, maybe I can be of some help there. I shall be able to reach the
> > author of PAML directly... shall I give it a try?
>
> Yes, please forward the patch - basically in the interest of the PAML
> authors themselves.

Sure!  In case you're afraid of colliding with Michael or
someone else, it's better to have a duplicate entry in a bug
tracker, and mark is as such, than no entry at all.  :)

Kind Regards,
--
Étienne Mollier <[hidden email]>
Fingerprint:  5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
Help find cures against the Covid-19 !  Give CPU cycles:
  * Rosetta@home: https://boinc.bakerlab.org/rosetta/
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--
Julien Y. Dutheil, Ph-D
0 (+49) 4522 763 298

§ Max Planck Institute for Evolutionary Biology
Molecular Systems Evolution
Department of Evolutionary Genetics
Plön -- GERMANY

§ Institute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE
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Re: RFS paml - fixed #957659

Étienne Mollier
Hi Julien,

Julien Yann Dutheil, on 2020-05-11 11:00:31 +0200:
> Got a reply from Ziheng Yang, the author of PAML. He said he will include
> the suggested changes upstream.

Great!  Thank you!

> PS: does this solve the issue or is there anything else I should do :s ?

I would be tempted to think that the issue is solved, both in
Debian and on upstream side.  Next update of PAML will most
likely include the correction, and the current patch on Debian
side will not apply anymore and will be simply dropped, which is
a good thing.

If you wish and your patch forwarding has been archived at some
public place, reading the DEP3[1], the URL could be used for
filling a "Bug:" field in the patch's metadata[2].  But if the
exchange occured on a private channel, I don't believe it is an
issue either: I tend to think the important thing is that the
upstream author has been made aware of the issue, and been
provided with the patch to mitigate it.

[1] https://dep-team.pages.debian.net/deps/dep3/
[2] https://salsa.debian.org/med-team/paml/-/blob/master/debian/patches/gcc10.patch

Have a nice day  :)
--
Étienne Mollier <[hidden email]>
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