Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Ole Streicher]

On 21.12.2016 19:16, Sandro Tosi wrote:
>> They are still, what the name suggests: candidates, with no confirmation
>> to be useful in a production environment. I don't see why they should
>> ever migrate to testing (as they did in 1.11.1rc.1). Last time, we had
>> an numpy RC in testing for more than four months (2016-05-06 to
>> 2016-10-16)! This doesn't confirm a sigh quality tendency. And imagine
> 
> this is the diff between 1.11.2rc1 and 1.11.2 (not the same versions
> you mentioned, but the most recent one we can make such comparison):
> 
> https://anonscm.debian.org/cgit/python-modules/packages/python-numpy.git/diff/?h=upstream/11.11.2

... and the difference to the one before is larger, and more critical,
and longer in testing.

> the version is just a name, there will be bugs even in the most shiny
> new release of every software

An "RC" instead of a release is there for a reason. The last (1.11)
numpy release process has shown that. It would be nice if the Debian
packaging would reflect this difference.

Best regards

Ole

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Sandro Tosi]

> They are still, what the name suggests: candidates, with no confirmation
> to be useful in a production environment. I don't see why they should
> ever migrate to testing (as they did in 1.11.1rc.1). Last time, we had
> an numpy RC in testing for more than four months (2016-05-06 to
> 2016-10-16)! This doesn't confirm a sigh quality tendency. And imagine

this is the diff between 1.11.2rc1 and 1.11.2 (not the same versions
you mentioned, but the most recent one we can make such comparison):

https://anonscm.debian.org/cgit/python-modules/packages/python-numpy.git/diff/?h=upstream/11.11.2

the version is just a name, there will be bugs even in the most shiny
new release of every software

> that happens now; chances are high that we release Stretch with a numpy
> release candidate.
>
> IMO the way numpy changes are to be tested in Debian needs some adjustment.



-- 
Sandro "morph" Tosi
My website: http://sandrotosi.me/
Me at Debian: http://wiki.debian.org/SandroTosi
G+: https://plus.google.com/u/0/+SandroTosi

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Ole Streicher]

Hi Sandro,

On 21.12.2016 16:43, Sandro Tosi wrote:
> On Wed, Dec 21, 2016 at 10:27 AM, Ole Streicher  wrote:
>> Sure; what I also don't understand is why numpy pushes its RC and betas
>> into unstable instead of experimental (and then maybe check or asks for
>> checking for the reverse deps). This makes it harder to revert if there
>> are problems.
>>
>> Sandro, maybe you could explain that a bit?
> 
> early/wider exposure, and they tend to be of high quality.

They are still, what the name suggests: candidates, with no confirmation
to be useful in a production environment. I don't see why they should
ever migrate to testing (as they did in 1.11.1rc.1). Last time, we had
an numpy RC in testing for more than four months (2016-05-06 to
2016-10-16)! This doesn't confirm a sigh quality tendency. And imagine
that happens now; chances are high that we release Stretch with a numpy
release candidate.

IMO the way numpy changes are to be tested in Debian needs some adjustment.

Best regards

Ole

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Sandro Tosi]

On Wed, Dec 21, 2016 at 10:27 AM, Ole Streicher  wrote:
> Sure; what I also don't understand is why numpy pushes its RC and betas
> into unstable instead of experimental (and then maybe check or asks for
> checking for the reverse deps). This makes it harder to revert if there
> are problems.
>
> Sandro, maybe you could explain that a bit?

early/wider exposure, and they tend to be of high quality.

-- 
Sandro "morph" Tosi
My website: http://sandrotosi.me/
Me at Debian: http://wiki.debian.org/SandroTosi
G+: https://plus.google.com/u/0/+SandroTosi

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Ole Streicher]

On 21.12.2016 16:17, Adrian Bunk wrote:
> I can clearly understand why Andreas is unhappy to see when such a 
> change is uploaded without prior warning 1.5 months after the start
> of the freeze, and 1 week before an important deadline for his package.

Sure; what I also don't understand is why numpy pushes its RC and betas
into unstable instead of experimental (and then maybe check or asks for
checking for the reverse deps). This makes it harder to revert if there
are problems.

Sandro, maybe you could explain that a bit?

Cheers

Ole

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Adrian Bunk]

On Wed, Dec 21, 2016 at 03:38:36PM +0100, Ole Streicher wrote:
> Hi Adrian,
> 
> On 21.12.2016 15:29, Adrian Bunk wrote:
> > On Wed, Dec 21, 2016 at 02:05:57PM +0100, Ole Streicher wrote:
> >> ...
> >> The according functions are since then marked as "deprecated" and issue
> >> a warning. Numpy introduced this change with 1.11rc already, which was
> >> uploaded to Debian about 6 months ago. After it appears that many
> >> packages (als in Debian) have problems with this, they postponed it for
> >> another release -- which happens just now.
> >> ...
> > 
> > You are saying you knew for 6 months that many packages in Debian
> > have problems with the changes that have just been uploaded.
> > 
> > Why were no bugs filed a few months before the upload?
> 
> Most of my own programs have CI tests which immediately gave a signal. I
> forwarded this upstream (mainly as github issues) and took part in the
> diskussion between upstream (f.e. astropy) and numpy, so that finally
> the decision was made to postpone.
> 
> Since I looked only on my own packages, there was no need to file bugs;
> especially since the problem was postponed. The upstream maintainers
> that were informed took measures in between; therefore I have only one
> package (astroml) currently failing.
> 
> I had no information about any other package; therefore I couldn't file
> bug reports. I can just recommend: If a Python package comes with tests,
> use the Debian CI infrastructure for it. This helps a lot as an early
> indicator of problems. And since the problems appear on packages with
> build time test, I would like to ask back: why don't you use CI?

I am not personally involved with python-skbio, but I can clearly 
understand why Andreas does not have the spare time to manually
check such things in all his packages:
  https://qa.debian.org/developer.php?login=ti...@debian.org

Looking at the CI logs for python-skbio, it also seems that breakages 
caused by pandas are the only ones that are visible there.

When tests fail in unstable there is very soon an RC bug from Lucas 
(this is the third such bug for python-skbio this year), so once the 
breakage is in unstable it anyway gets reported pretty quickly.

I can clearly understand why Andreas is unhappy to see when such a 
change is uploaded without prior warning 1.5 months after the start
of the freeze, and 1 week before an important deadline for his package.

> Best regards
> 
> Ole

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed


-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Ole Streicher]

Hi Adrian,

On 21.12.2016 15:29, Adrian Bunk wrote:
> On Wed, Dec 21, 2016 at 02:05:57PM +0100, Ole Streicher wrote:
>> ...
>> The according functions are since then marked as "deprecated" and issue
>> a warning. Numpy introduced this change with 1.11rc already, which was
>> uploaded to Debian about 6 months ago. After it appears that many
>> packages (als in Debian) have problems with this, they postponed it for
>> another release -- which happens just now.
>> ...
> 
> You are saying you knew for 6 months that many packages in Debian
> have problems with the changes that have just been uploaded.
> 
> Why were no bugs filed a few months before the upload?

Most of my own programs have CI tests which immediately gave a signal. I
forwarded this upstream (mainly as github issues) and took part in the
diskussion between upstream (f.e. astropy) and numpy, so that finally
the decision was made to postpone.

Since I looked only on my own packages, there was no need to file bugs;
especially since the problem was postponed. The upstream maintainers
that were informed took measures in between; therefore I have only one
package (astroml) currently failing.

I had no information about any other package; therefore I couldn't file
bug reports. I can just recommend: If a Python package comes with tests,
use the Debian CI infrastructure for it. This helps a lot as an early
indicator of problems. And since the problems appear on packages with
build time test, I would like to ask back: why don't you use CI?

Best regards

Ole

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Adrian Bunk]

On Wed, Dec 21, 2016 at 02:05:57PM +0100, Ole Streicher wrote:
>...
> The according functions are since then marked as "deprecated" and issue
> a warning. Numpy introduced this change with 1.11rc already, which was
> uploaded to Debian about 6 months ago. After it appears that many
> packages (als in Debian) have problems with this, they postponed it for
> another release -- which happens just now.
>...

You are saying you knew for 6 months that many packages in Debian
have problems with the changes that have just been uploaded.

Why were no bugs filed a few months before the upload?

> Best regards
> 
> Ole

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed


-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Adrian Bunk]

On Wed, Dec 21, 2016 at 07:54:35AM -0500, Sandro Tosi wrote:
>...
> > On Wed, Dec 21, 2016 at 11:40:16AM +0200, Adrian Bunk wrote:
>...
> >> For python-skbio to have any chance of being part of stretch, the
> >> latest possible date for an upload of a package without any RC bugs
> >> is Christmas Day (and then not touch the package for 10 days).
> >>
> >> If this issue is not resolved by Christmas, your Christmas present for
> >> the python-skbio maintainers is that their package will definitely not
> >> be part of stretch.
> 
> sarcasm wont help you make your point.

My point was how wrong your "there is still a month to the freeze" was.

And as a matter of fact, the freeze did already start 1.5 months ago 
with the transition freeze.

>...
> * engage with upstream to get this fixed by them and backport the
> patch to the current package (if they prefer not to release a new
> version now)

I'm glad I am not involved with any of the affected packages.

3 days before Christmas Eve is approximately the worst time of the year 
when you need something urgently from other people.

> * skip that test / dont make the build fail if there is a test failure
> (for now!).

In practice, "for now" means "forever".

Do you really want to recommend to people to disable failing tests 
in cases where these are showing real bugs in the code?

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed


-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Sandro Tosi]

On Wed, Dec 21, 2016 at 8:35 AM, Andreas Tille  wrote:
> In my initial response I mentioned skiping the test.  However, I
> intended to discuss this first since simply hiding the eyes from an
> upgrading problem is not the prefered way to go.

youre not closing your eyes to a problem: you find one, you recognize
there is one, and that you cant work on it right now, so skipping that
test is actually a very evident way of say "it's on my radar, will
work on it"

-- 
Sandro "morph" Tosi
My website: http://sandrotosi.me/
Me at Debian: http://wiki.debian.org/SandroTosi
G+: https://plus.google.com/u/0/+SandroTosi

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Andreas Tille]

Hi Ole,

On Wed, Dec 21, 2016 at 02:05:57PM +0100, Ole Streicher wrote:
> On 21.12.2016 11:59, Andreas Tille wrote:
> > On Wed, Dec 21, 2016 at 11:40:16AM +0200, Adrian Bunk wrote:
> >> For python-skbio it is *really* time to panic *right now*.
> > Thanks for confirming that I was not actually panicing. ;-)
> 
> While I agree in principle, I would like to remind the following as well:
> 
> The current FTBFS mainly (as far as I can see) come from a change that
> was announced already two numpy versions ago: that numpy will refuse to
> accept floats as indices.
> 
> The according functions are since then marked as "deprecated" and issue
> a warning. Numpy introduced this change with 1.11rc already, which was
> uploaded to Debian about 6 months ago. After it appears that many
> packages (als in Debian) have problems with this, they postponed it for
> another release -- which happens just now.

Thanks for the information.  However, you know that not all upstreams
are following these changes in a timely manner and not every maintainer
is following the changes of the reverse dependencies that closely.  In
any case we have a transition freeze and my point was *also* to check
whether there are other rdepends of Numpy.  I admit that python-skbio is
a low popcon package and if there are no other problems with the new
Numpy verision *and* the new version has large advantages over the old
one *and* is as RC candidate stable enough to go into Stretch its
probably not a big deal if we backport python-skbio.
 
> I am a bin angry here about unresponsive upstreams, which just ignore
> these changes as long as possible, and I am not sure whether we should
> ship Stretch with an outdated numpy release

As far as I can see the current stable is 1.11.2 the current target for
Stretch is just an RC candidate.

> (I am too lazy in the moment to support my statement with links; if you
> need, I will do so ofcourse)

I fully believe you without links. :-)

Kind regards

 Andreas.

-- 
http://fam-tille.de

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Andreas Tille]

Hi Sandro,

On Wed, Dec 21, 2016 at 07:54:35AM -0500, Sandro Tosi wrote:
> On Wed, Dec 21, 2016 at 5:59 AM, Andreas Tille  wrote:
> >> For python-skbio it is *really* time to panic *right now*.
> >>
> >> python-skbio is currently not in testing.
> 
> the last upload (0.5.1-1) was done on Nov 19 and skbio hasnt been in
> testing for more than 11 months. if it hasnt reached testing by now,
> it must have had several other issues.

Its correct that it *had* issues in the past - but that's what we were
working on and we had assumed that all issues are solved now.
 
> >> If this issue is not resolved by Christmas, your Christmas present for
> >> the python-skbio maintainers is that their package will definitely not
> >> be part of stretch.
> 
> sarcasm wont help you make your point.

I agree that sarcasm does not help.  However, we were really aiming at
having skbio in stretch.
 
> > Thanks for confirming that I was not actually panicing. ;-)
> >
> > Sandro, would you reconsider my suggestion to revert this
> > mini-transition?  I do not see a realistic chance that upstream will
> > come up with fixes in the next two days.
> 
> how did you reach this conclusion? before i reported this bug upstream
> (why didnt you do it?) they probably werent even aware of the issue.

Thanks for contacting upstream.  I confirm that I planed to do this but
several other bugs droped in yesterday and I did not manage.
 
> I think you have multiple actions you can do:
> 
> * actually investigate what the issue is, did you try to do it? you
> might also find out the fix is easy and end up submitting a patch
> upstream
> * engage with upstream to get this fixed by them and backport the
> patch to the current package (if they prefer not to release a new
> version now)
> * skip that test / dont make the build fail if there is a test failure
> (for now!). Test suites are made to catch errors, and in this case it
> worked! expecting the test suite to pass every time is either
> unrealistic or an indication the suite is too shallow. grab
> information about the failure and report them upstream, but in the
> meantime (since it's a known issue) you can decide to skip the failure

In my initial response I mentioned skiping the test.  However, I
intended to discuss this first since simply hiding the eyes from an
upgrading problem is not the prefered way to go.
 
> you say you are in a hurry, and yet you decided to waste a whole day
> in this blame-game, i'm sure there is much more you can do to fix
> skbio.

Sandro, please calm down.  I did not tried to play a blame-game. I was
busy fixing other RC bugs.  I was considering it a 50% chance that a
mini-transition might be reverted and thus I started with other packages
where 100% action was needed.  I also need to admit that I do not feel
competent in Numpy details that the time-effort investment for myself
makes the time well spent (compared to other tasks).

Kind regards

 Andreas.

-- 
http://fam-tille.de

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Ole Streicher]

Hi all,

On 21.12.2016 11:59, Andreas Tille wrote:
> On Wed, Dec 21, 2016 at 11:40:16AM +0200, Adrian Bunk wrote:
>> For python-skbio it is *really* time to panic *right now*.
> Thanks for confirming that I was not actually panicing. ;-)

While I agree in principle, I would like to remind the following as well:

The current FTBFS mainly (as far as I can see) come from a change that
was announced already two numpy versions ago: that numpy will refuse to
accept floats as indices.

The according functions are since then marked as "deprecated" and issue
a warning. Numpy introduced this change with 1.11rc already, which was
uploaded to Debian about 6 months ago. After it appears that many
packages (als in Debian) have problems with this, they postponed it for
another release -- which happens just now.

I am a bin angry here about unresponsive upstreams, which just ignore
these changes as long as possible, and I am not sure whether we should
ship Stretch with an outdated numpy release just because there are a
number of upstreams that are too lazy to keep their packages up to date.
I would really ask to push upstream hardly to do the required changes;
maybe we can decide if it is needed to revert that later. The changes
are required anyway; doing them sooner than later is no mistake in any case.

(I am too lazy in the moment to support my statement with links; if you
need, I will do so ofcourse)

Best regards

Ole

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Sandro Tosi]

On Wed, Dec 21, 2016 at 5:59 AM, Andreas Tille  wrote:
> Hi Adrian and Anton,
>
> On Wed, Dec 21, 2016 at 11:40:16AM +0200, Adrian Bunk wrote:
>> On Tue, Dec 20, 2016 at 09:01:31AM -0500, Sandro Tosi wrote:
>> > > it seems the recent upgrade of numpy has broken some tests in other
>> > > packages like for instance this one in python-skbio.  I wonder whether
>> > > you are either able to suggest patches to get the tests working with the
>> > > new interface of numpy again or whether it might be sensible to revert
>> > > the upgrade of python-numpy to the previous version considering that we
>> > > are quite close to the freeze.
>> >
>> > There is still a month to the freeze for the existing package, so
>> > let's not panic already. I'd suggest contacting the upstream of the
>> > projects with failing test and ask for support
>>
>> For python-skbio it is *really* time to panic *right now*.
>>
>> python-skbio is currently not in testing.

the last upload (0.5.1-1) was done on Nov 19 and skbio hasnt been in
testing for more than 11 months. if it hasnt reached testing by now,
it must have had several other issues.

>>
>> For python-skbio to have any chance of being part of stretch, the
>> latest possible date for an upload of a package without any RC bugs
>> is Christmas Day (and then not touch the package for 10 days).
>>
>> If this issue is not resolved by Christmas, your Christmas present for
>> the python-skbio maintainers is that their package will definitely not
>> be part of stretch.

sarcasm wont help you make your point.

>
> Thanks for confirming that I was not actually panicing. ;-)
>
> Sandro, would you reconsider my suggestion to revert this
> mini-transition?  I do not see a realistic chance that upstream will
> come up with fixes in the next two days.

how did you reach this conclusion? before i reported this bug upstream
(why didnt you do it?) they probably werent even aware of the issue.

I think you have multiple actions you can do:

* actually investigate what the issue is, did you try to do it? you
might also find out the fix is easy and end up submitting a patch
upstream
* engage with upstream to get this fixed by them and backport the
patch to the current package (if they prefer not to release a new
version now)
* skip that test / dont make the build fail if there is a test failure
(for now!). Test suites are made to catch errors, and in this case it
worked! expecting the test suite to pass every time is either
unrealistic or an indication the suite is too shallow. grab
information about the failure and report them upstream, but in the
meantime (since it's a known issue) you can decide to skip the failure

you say you are in a hurry, and yet you decided to waste a whole day
in this blame-game, i'm sure there is much more you can do to fix
skbio.

-- 
Sandro "morph" Tosi
My website: http://sandrotosi.me/
Me at Debian: http://wiki.debian.org/SandroTosi
G+: https://plus.google.com/u/0/+SandroTosi

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Andreas Tille]

Hi Adrian and Anton,

On Wed, Dec 21, 2016 at 11:40:16AM +0200, Adrian Bunk wrote:
> On Tue, Dec 20, 2016 at 09:01:31AM -0500, Sandro Tosi wrote:
> > > it seems the recent upgrade of numpy has broken some tests in other
> > > packages like for instance this one in python-skbio.  I wonder whether
> > > you are either able to suggest patches to get the tests working with the
> > > new interface of numpy again or whether it might be sensible to revert
> > > the upgrade of python-numpy to the previous version considering that we
> > > are quite close to the freeze.
> > 
> > There is still a month to the freeze for the existing package, so
> > let's not panic already. I'd suggest contacting the upstream of the
> > projects with failing test and ask for support
> 
> For python-skbio it is *really* time to panic *right now*.
> 
> python-skbio is currently not in testing.
> 
> For python-skbio to have any chance of being part of stretch, the
> latest possible date for an upload of a package without any RC bugs
> is Christmas Day (and then not touch the package for 10 days).
> 
> If this issue is not resolved by Christmas, your Christmas present for 
> the python-skbio maintainers is that their package will definitely not
> be part of stretch.

Thanks for confirming that I was not actually panicing. ;-)

Sandro, would you reconsider my suggestion to revert this
mini-transition?  I do not see a realistic chance that upstream will
come up with fixes in the next two days.

Kind regards

  Andreas.

-- 
http://fam-tille.de

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Bug#848758: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Adrian Bunk]

On Tue, Dec 20, 2016 at 09:01:31AM -0500, Sandro Tosi wrote:
> > it seems the recent upgrade of numpy has broken some tests in other
> > packages like for instance this one in python-skbio.  I wonder whether
> > you are either able to suggest patches to get the tests working with the
> > new interface of numpy again or whether it might be sensible to revert
> > the upgrade of python-numpy to the previous version considering that we
> > are quite close to the freeze.
> 
> There is still a month to the freeze for the existing package, so
> let's not panic already. I'd suggest contacting the upstream of the
> projects with failing test and ask for support

For python-skbio it is *really* time to panic *right now*.

python-skbio is currently not in testing.

For python-skbio to have any chance of being part of stretch, the
latest possible date for an upload of a package without any RC bugs
is Christmas Day (and then not touch the package for 10 days).

If this issue is not resolved by Christmas, your Christmas present for 
the python-skbio maintainers is that their package will definitely not
be part of stretch.

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed


-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Anton Gladky]

2016-12-20 15:01 GMT+01:00 Sandro Tosi :
>> it seems the recent upgrade of numpy has broken some tests in other
>> packages like for instance this one in python-skbio.  I wonder whether
>> you are either able to suggest patches to get the tests working with the
>> new interface of numpy again or whether it might be sensible to revert
>> the upgrade of python-numpy to the previous version considering that we
>> are quite close to the freeze.
>
> There is still a month to the freeze for the existing package, so
> let's not panic already. I'd suggest contacting the upstream of the
> projects with failing test and ask for support

I do support Andreas' statement and ask to revert numpy upload if patches
for the dependent packages are not available. We are too close to the freeze
to fix many new bugs and Christmas time will unlikely motivate upstream people
to fix new "numpy API". Semi-transitions should be avoided already.

Thanks

Anton

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Re: Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Sandro Tosi]

> it seems the recent upgrade of numpy has broken some tests in other
> packages like for instance this one in python-skbio.  I wonder whether
> you are either able to suggest patches to get the tests working with the
> new interface of numpy again or whether it might be sensible to revert
> the upgrade of python-numpy to the previous version considering that we
> are quite close to the freeze.

There is still a month to the freeze for the existing package, so
let's not panic already. I'd suggest contacting the upstream of the
projects with failing test and ask for support


-- 
Sandro "morph" Tosi
My website: http://sandrotosi.me/
Me at Debian: http://wiki.debian.org/SandroTosi
G+: https://plus.google.com/u/0/+SandroTosi

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers

Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Andreas Tille]

[Debian Science maintainers and Debian Med packaging in CC as warning]

Hi Sandro,

it seems the recent upgrade of numpy has broken some tests in other
packages like for instance this one in python-skbio.  I wonder whether
you are either able to suggest patches to get the tests working with the
new interface of numpy again or whether it might be sensible to revert
the upgrade of python-numpy to the previous version considering that we
are quite close to the freeze.

Kind regards

Andreas.

On Mon, Dec 19, 2016 at 10:19:10PM +0100, Lucas Nussbaum wrote:
> Source: python-skbio
> Version: 0.5.1-1
> Severity: serious
> Tags: stretch sid
> User: debian...@lists.debian.org
> Usertags: qa-ftbfs-20161219 qa-ftbfs
> Justification: FTBFS on amd64
> 
> Hi,
> 
> During a rebuild of all packages in sid, your package failed to build on
> amd64.
> 
> Relevant part (hopefully):
> > multiple_comparisons_correction=None)
> >   File 
> > "/<>/.pybuild/pythonX.Y_3.5/build/skbio/stats/composition.py", 
> > line 971, in ancom
> > _logratio_mat = _log_compare(mat.values, cats.values, significance_test)
> >   File 
> > "/<>/.pybuild/pythonX.Y_3.5/build/skbio/stats/composition.py", 
> > line 1084, in _log_compare
> > arr=ratio)
> >   File "/usr/lib/python3/dist-packages/numpy/lib/shape_base.py", line 133, 
> > in apply_along_axis
> > if res.shape == ():
> > AttributeError: 'F_onewayResult' object has no attribute 'shape'
> > 
> > --
> > Ran 2238 tests in 42.139s
> > 
> > FAILED (SKIP=30, errors=15)
> > E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1: cd 
> > /<>/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose 
> > dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned 
> > exit code 13
> > debian/rules:22: recipe for target 'override_dh_auto_test' failed
> 
> The full build log is available from:
>http://aws-logs.debian.net/2016/12/19/python-skbio_0.5.1-1_unstable.log
> 
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
> 
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
> 
> ___
> Debian-med-packaging mailing list
> debian-med-packag...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> 

-- 
http://fam-tille.de

-- 
debian-science-maintainers mailing list
debian-science-maintainers@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers