Bug#909990: nibabel: FTBFS (Failed example)

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Bug#909990: nibabel: FTBFS (Failed example)

Santiago Vila-2
Package: src:nibabel
Version: 2.3.0-1
Severity: serious
Tags: ftbfs

Dear maintainer:

I tried to build this package in buster but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep --buildsystem=python_distutils --builddirectory=build --with=python2,python3
   dh_update_autotools_config -i -O--buildsystem=python_distutils -O--builddirectory=build
   dh_auto_configure -i -O--buildsystem=python_distutils -O--builddirectory=build
dh_auto_configure: Please use the third-party "pybuild" build system instead of python-distutils
dh_auto_configure: This feature will be removed in compat 12.
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
dh_auto_build: Please use the third-party "pybuild" build system instead of python-distutils
dh_auto_build: This feature will be removed in compat 12.
        python setup.py build --force
Missing optional package "dicom" provided by package "pydicom"; you may get run-time errors
running build

[... snipped ...]

  dslice = dslice.astype(out_dtype)
./<<PKGBUILDDIR>>/nibabel/volumeutils.py:818: ComplexWarning: Casting complex values to real discards the imaginary part
  dslice = dslice.astype(in_cast)
........................................................
======================================================================
FAIL: Doctest: nibabel.deprecated.FutureWarningMixin
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.7/doctest.py", line 2198, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for nibabel.deprecated.FutureWarningMixin
  File "/<<PKGBUILDDIR>>/nibabel/deprecated.py", line 42, in FutureWarningMixin

----------------------------------------------------------------------
File "/<<PKGBUILDDIR>>/nibabel/deprecated.py", line 53, in nibabel.deprecated.FutureWarningMixin
Failed example:
    with warnings.catch_warnings(record=True) as warns:
        d = D()
        warns[0].message
Expected:
    FutureWarning("Please, don't use this class",)
Got:
    FutureWarning("Please, don't use this class")


======================================================================
FAIL: nibabel.tests.test_testing.test_clear_and_catch_warnings
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/<<PKGBUILDDIR>>/nibabel/tests/test_testing.py", line 89, in test_clear_and_catch_warnings
    assert_warn_len_equal(my_mod, 1)
  File "/<<PKGBUILDDIR>>/nibabel/tests/test_testing.py", line 72, in assert_warn_len_equal
    assert_equal(len(mod_warns), 2)  # including 'version'
AssertionError: 1 != 2

----------------------------------------------------------------------
Ran 7721 tests in 68.265s

FAILED (SKIP=55, failures=2)
make[2]: *** [Makefile:94: unittest] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [debian/rules:43: python-test3.7] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:18: build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep subprocess returned exit status 2
--------------------------------------------------------------------------------

The build was made in my autobuilder with "dpkg-buildpackage -A"
but it also fails here:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/nibabel.html

where you can get a full build log if you need it.

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.

Thanks.

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Andreas Tille-5
Hi,

to see what I can do about bug #909990 I've imported the latest version
into the packaging Git[1].  When beeing inside the main dir of the Git
repository I can easily do

neurodebian-team/pynifti(debian) $ python3
Python 3.6.6 (default, Jun 27 2018, 14:44:17)
[GCC 8.1.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import nibabel
>>>

However, if I try inside the .pybuild dir I get:

/build/nibabel-2.3.0/.pybuild/cpython3_3.6_nibabel/build# python3.6
Python 3.6.7rc1 (default, Sep 27 2018, 09:51:25)
[GCC 8.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import nibabel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/build/nibabel-2.3.0/.pybuild/cpython3_3.6_nibabel/build/nibabel/__init__.py", line 45, in <module>
    from .loadsave import load, save
  File "/build/nibabel-2.3.0/.pybuild/cpython3_3.6_nibabel/build/nibabel/loadsave.py", line 18, in <module>
    from .imageclasses import all_image_classes
  File "/build/nibabel-2.3.0/.pybuild/cpython3_3.6_nibabel/build/nibabel/imageclasses.py", line 16, in <module>
    from .minc1 import Minc1Image
  File "/build/nibabel-2.3.0/.pybuild/cpython3_3.6_nibabel/build/nibabel/minc1.py", line 20, in <module>
    from .deprecated import FutureWarningMixin
ImportError: cannot import name 'FutureWarningMixin'
>>>      


This leads to errors when the build process is trying to create the
docs via

  export PYTHONPATH=`pybuild --print build_dir --interpreter python3` ; \
  cd doc && /usr/bin/make html-only

(which triggers exactly the above error message).

Any idea what might went wrong here?  Its definitely not the slightly
different Python 3.6 version - I tried a local build using 3.6.6 with
the very same effect.

Kind regards

       Andreas.

[1] Vcs-Git: https://salsa.debian.org/neurodebian-team/pynifti.git -b debian
    (yes, I switched to Branch debian instead of current package 2.3.0-1
     which has non-default Branch dist/debian/proper)

--
http://fam-tille.de

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Andreas Tille-2
In reply to this post by Santiago Vila-2
Hi Yaroslav,

On Mon, Oct 08, 2018 at 11:25:53AM -0400, Yaroslav Halchenko wrote:
> Thank you Andreas for looking into it

You are welcome.

> 2.3.1 bugfix is around the corner
> https://github.com/nipy/nibabel/pull/667
> so I will aim to make sure the #909990 is fixed within it (for starters
> - I do not think I observed this exception when building from current RC
>   branch)

I used this as quilt patch and the package builds now (after I excluded
another quite suspicious test in a quilt patch).  The package builds now
and I've team uploaded to unstable.

BTW, I'd consider it more straightforward if the repository would be
renamed from

   https://salsa.debian.org/neurodebian-team/pynifti

to

   https://salsa.debian.org/neurodebian-team/nibabel

since I would expect the repository named like the source package (and
some Blends tools are half way relying on this).

Kind regards

      Andreas.

--
http://fam-tille.de

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Yaroslav Halchenko-9

On Tue, 09 Oct 2018, Andreas Tille wrote:

> > 2.3.1 bugfix is around the corner
> > https://github.com/nipy/nibabel/pull/667
> > so I will aim to make sure the #909990 is fixed within it (for starters
> > - I do not think I observed this exception when building from current RC
> >   branch)

> I used this as quilt patch and the package builds now (after I excluded
> another quite suspicious test in a quilt patch).  The package builds now
> and I've team uploaded to unstable.

ok... will merge for the next upload to proceed -- we mitigated all
known issues, and the beast builds fine all the way down to jessie, so
release is coming soon now

> BTW, I'd consider it more straightforward if the repository would be
> renamed from

>    https://salsa.debian.org/neurodebian-team/pynifti

> to

>    https://salsa.debian.org/neurodebian-team/nibabel

> since I would expect the repository named like the source package (and
> some Blends tools are half way relying on this).

good idea, done

will commit now adjustment to debian/control

--
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik       

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Yaroslav Halchenko-9

On Fri, 12 Oct 2018, Yaroslav Halchenko wrote:


> On Tue, 09 Oct 2018, Andreas Tille wrote:

> > > 2.3.1 bugfix is around the corner
> > > https://github.com/nipy/nibabel/pull/667
> > > so I will aim to make sure the #909990 is fixed within it (for starters
> > > - I do not think I observed this exception when building from current RC
> > >   branch)

> > I used this as quilt patch and the package builds now (after I excluded
> > another quite suspicious test in a quilt patch).  The package builds now
> > and I've team uploaded to unstable.

> ok... will merge for the next upload to proceed -- we mitigated all
> known issues, and the beast builds fine all the way down to jessie, so
> release is coming soon now

oi... I guess we caused you confusion and unneeded work???

I see that you updated debian branch redoing packaging for 2.3.0-1 which was
uploaded already awhile back, while we use this ad-hoc dist/debian/proper
branch (should be the default when you clone that repo):

$> grep Vcs-Git debian/control
Vcs-Git: https://salsa.debian.org/neurodebian-team/pynifti.git -b dist/debian/proper

so not yet sure how to proceed with your changes. meanwhile pushed my local
state of dist/debian/proper

--
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik       

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Andreas Tille-2
On Fri, Oct 12, 2018 at 09:15:37AM -0400, Yaroslav Halchenko wrote:
> > ok... will merge for the next upload to proceed -- we mitigated all
> > known issues, and the beast builds fine all the way down to jessie, so
> > release is coming soon now
>
> oi... I guess we caused you confusion and unneeded work???

Urgs, yes! While I for sure need to blame myself that I missed to check
the diff between repository and uploads, your naming of branches is
irritating.
 
> I see that you updated debian branch redoing packaging for 2.3.0-1 which was
> uploaded already awhile back, while we use this ad-hoc dist/debian/proper
> branch (should be the default when you clone that repo):

Could you imagine to use a branch named debian?  In my attempt to update
packages mentioned in Debian Med tasks which are not uploaded for a long
time and need fixing Vcs fields (and usually lots of lintian issues) I
migrated pyepl to the "kind of usual" repository layout.  Do you have
some tools that are relying on those unusual names (= did I broke
something when renaming dist/debian/proper to debian in pyepl)?
 
> $> grep Vcs-Git debian/control
> Vcs-Git: https://salsa.debian.org/neurodebian-team/pynifti.git -b dist/debian/proper
>
> so not yet sure how to proceed with your changes. meanwhile pushed my local
> state of dist/debian/proper

I'd volunteer to check the diff between your current changes and my work
and merge everything - but can I please use a branch named debian?

Kind regards

       Andreas.

--
http://fam-tille.de

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Yaroslav Halchenko-9

On Sat, 13 Oct 2018, Andreas Tille wrote:

> On Fri, Oct 12, 2018 at 09:15:37AM -0400, Yaroslav Halchenko wrote:
> > > ok... will merge for the next upload to proceed -- we mitigated all
> > > known issues, and the beast builds fine all the way down to jessie, so
> > > release is coming soon now

> > oi... I guess we caused you confusion and unneeded work???

> Urgs, yes! While I for sure need to blame myself that I missed to check
> the diff between repository and uploads, your naming of branches is
> irritating.

> > I see that you updated debian branch redoing packaging for 2.3.0-1 which was
> > uploaded already awhile back, while we use this ad-hoc dist/debian/proper
> > branch (should be the default when you clone that repo):

> Could you imagine to use a branch named debian?  In my attempt to update
> packages mentioned in Debian Med tasks which are not uploaded for a long
> time and need fixing Vcs fields (and usually lots of lintian issues) I
> migrated pyepl to the "kind of usual" repository layout.  Do you have
> some tools that are relying on those unusual names (= did I broke
> something when renaming dist/debian/proper to debian in pyepl)?

> > $> grep Vcs-Git debian/control
> > Vcs-Git: https://salsa.debian.org/neurodebian-team/pynifti.git -b dist/debian/proper

> > so not yet sure how to proceed with your changes. meanwhile pushed my local
> > state of dist/debian/proper

> I'd volunteer to check the diff between your current changes and my work
> and merge everything - but can I please use a branch named debian?

quick one:  well, the main confusion stems from that fact that
originally it was pynifti project and there is still that debian branch
for its packaging, which I thought would be the one up to date with

$> apt-cache policy python-nifti
python-nifti:
  Installed: (none)
  Candidate: 0.20100607.1-4.1
  Version table:
     0.20100607.1-4.1 600
        100 http://http.debian.net/debian stretch/main amd64 Packages
        600 http://http.debian.net/debian sid/main amd64 Packages
     0.20100607.1-4~nd70+1+nd90+1 500
        500 http://neuro.debian.net/debian stretch/main amd64 Packages

but now I don't know -- locally it is stuck somewhere in 2009.  So, sure
-- could be 'debian' for what I care

--
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik       

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Andreas Tille-2
Hi Yaroslav,

On Sat, Oct 13, 2018 at 08:29:53PM -0400, Yaroslav Halchenko wrote:

>
> > I'd volunteer to check the diff between your current changes and my work
> > and merge everything - but can I please use a branch named debian?
>
> quick one:  well, the main confusion stems from that fact that
> originally it was pynifti project and there is still that debian branch
> for its packaging, which I thought would be the one up to date with
>
> $> apt-cache policy python-nifti
> python-nifti:
>   Installed: (none)
>   Candidate: 0.20100607.1-4.1
>   Version table:
>      0.20100607.1-4.1 600
>         100 http://http.debian.net/debian stretch/main amd64 Packages
>         600 http://http.debian.net/debian sid/main amd64 Packages
>      0.20100607.1-4~nd70+1+nd90+1 500
>         500 http://neuro.debian.net/debian stretch/main amd64 Packages
>
> but now I don't know -- locally it is stuck somewhere in 2009.  So, sure
> -- could be 'debian' for what I care

I took your word as confirmation to restructure the repository.
Moreover I have ported all my changes to this repository.  I have also
seen that you commited some git state.  I have used git mode in watch
file to easily fetch the latest HEAD from upstream and at the same time
be able to use Debian tools.  I have not tagged the status as upload
since it might be better if you have a final review.

Kind regards

       Andreas.

--
http://fam-tille.de

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Yaroslav Halchenko-9

On Sun, 14 Oct 2018, Andreas Tille wrote:

> Hi Yaroslav,

> On Sat, Oct 13, 2018 at 08:29:53PM -0400, Yaroslav Halchenko wrote:

> > > I'd volunteer to check the diff between your current changes and my work
> > > and merge everything - but can I please use a branch named debian?

> > quick one:  well, the main confusion stems from that fact that
> > originally it was pynifti project and there is still that debian branch
> > for its packaging, which I thought would be the one up to date with

> > $> apt-cache policy python-nifti
> > python-nifti:
> >   Installed: (none)
> >   Candidate: 0.20100607.1-4.1
> >   Version table:
> >      0.20100607.1-4.1 600
> >         100 http://http.debian.net/debian stretch/main amd64 Packages
> >         600 http://http.debian.net/debian sid/main amd64 Packages
> >      0.20100607.1-4~nd70+1+nd90+1 500
> >         500 http://neuro.debian.net/debian stretch/main amd64 Packages

> > but now I don't know -- locally it is stuck somewhere in 2009.  So, sure
> > -- could be 'debian' for what I care

> I took your word as confirmation to restructure the repository.
> Moreover I have ported all my changes to this repository.  I have also
> seen that you commited some git state.  I have used git mode in watch
> file to easily fetch the latest HEAD from upstream and at the same time
> be able to use Debian tools.  I have not tagged the status as upload
> since it might be better if you have a final review.

Yet to look at your changes, but for now I have

- pushed debian/2.3.1-1  packaging (withing "old" custom
  "on top of upstream releases in git" dist/debian/proper branch)

- force-pushed  

        $> git push -f  salsa debian/2.3.0-1 2.3.0    
        Enumerating objects: 1, done.
        Counting objects: 100% (1/1), done.
        Writing objects: 100% (1/1), 828 bytes | 828.00 KiB/s, done.
        Total 1 (delta 0), reused 0 (delta 0)
        To salsa.debian.org:neurodebian-team/nibabel.git
         + 3bb95b3b...1ea63921 2.3.0 -> 2.3.0 (forced update)
         + 62f64245...8519cb3d debian/2.3.0-1 -> debian/2.3.0-1 (forced update)

so they correspond to the previous release which we already had in debian.

--
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik       

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Yaroslav Halchenko-9

On Thu, 18 Oct 2018, Yaroslav Halchenko wrote:

> Yet to look at your changes, but for now I have

> - pushed debian/2.3.1-1  packaging (withing "old" custom
>   "on top of upstream releases in git" dist/debian/proper branch)

> - force-pushed  

> $> git push -f  salsa debian/2.3.0-1 2.3.0    
> Enumerating objects: 1, done.
> Counting objects: 100% (1/1), done.
> Writing objects: 100% (1/1), 828 bytes | 828.00 KiB/s, done.
> Total 1 (delta 0), reused 0 (delta 0)
> To salsa.debian.org:neurodebian-team/nibabel.git
> + 3bb95b3b...1ea63921 2.3.0 -> 2.3.0 (forced update)
> + 62f64245...8519cb3d debian/2.3.0-1 -> debian/2.3.0-1 (forced update)

> so they correspond to the previous release which we already had in debian.

oh now it is a mess -- I have missed the fact that you uploaded a
snapshot  2.3.0+git20181012.791678e-1  to Debian...

--
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik       

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Andreas Tille-2
On Thu, Oct 18, 2018 at 09:21:37AM -0400, Yaroslav Halchenko wrote:

>
> On Thu, 18 Oct 2018, Yaroslav Halchenko wrote:
>
> > Yet to look at your changes, but for now I have
>
> > - pushed debian/2.3.1-1  packaging (withing "old" custom
> >   "on top of upstream releases in git" dist/debian/proper branch)
>
> > - force-pushed  
>
> > $> git push -f  salsa debian/2.3.0-1 2.3.0    
> > Enumerating objects: 1, done.
> > Counting objects: 100% (1/1), done.
> > Writing objects: 100% (1/1), 828 bytes | 828.00 KiB/s, done.
> > Total 1 (delta 0), reused 0 (delta 0)
> > To salsa.debian.org:neurodebian-team/nibabel.git
> > + 3bb95b3b...1ea63921 2.3.0 -> 2.3.0 (forced update)
> > + 62f64245...8519cb3d debian/2.3.0-1 -> debian/2.3.0-1 (forced update)
>
> > so they correspond to the previous release which we already had in debian.
>
> oh now it is a mess -- I have missed the fact that you uploaded a
> snapshot  2.3.0+git20181012.791678e-1  to Debian...

I hope this will not create any trouble.  I assumed you would follow Git
HEAD.  if not the watch file needs to be reverted.

Sorry if I might have created work instead of lending a helping hand.

Kind regards

       Andreas.

--
http://fam-tille.de

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Bug#909990: Stange import error for nibabel when trying to import from .pybuild

Yaroslav Halchenko-9

On Thu, 18 Oct 2018, Andreas Tille wrote:

> On Thu, Oct 18, 2018 at 09:21:37AM -0400, Yaroslav Halchenko wrote:

> > On Thu, 18 Oct 2018, Yaroslav Halchenko wrote:

> > > Yet to look at your changes, but for now I have

> > > - pushed debian/2.3.1-1  packaging (withing "old" custom
> > >   "on top of upstream releases in git" dist/debian/proper branch)

> > > - force-pushed  

> > > $> git push -f  salsa debian/2.3.0-1 2.3.0    
> > > Enumerating objects: 1, done.
> > > Counting objects: 100% (1/1), done.
> > > Writing objects: 100% (1/1), 828 bytes | 828.00 KiB/s, done.
> > > Total 1 (delta 0), reused 0 (delta 0)
> > > To salsa.debian.org:neurodebian-team/nibabel.git
> > > + 3bb95b3b...1ea63921 2.3.0 -> 2.3.0 (forced update)
> > > + 62f64245...8519cb3d debian/2.3.0-1 -> debian/2.3.0-1 (forced update)

> > > so they correspond to the previous release which we already had in debian.

> > oh now it is a mess -- I have missed the fact that you uploaded a
> > snapshot  2.3.0+git20181012.791678e-1  to Debian...

> I hope this will not create any trouble.  I assumed you would follow Git
> HEAD.  if not the watch file needs to be reverted.

I don't think revertions would be needed, but we would need to merge the
two

> Sorry if I might have created work instead of lending a helping hand.

life is life ;-)  regardless, thanks for your work!

--
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik       

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