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Re: foo FTBFS with dh-python >= 3.20180313

Started byPiotr Ożarowski <piotr@debian.org>
First post2018-04-26 12:10 +0200
Last post2018-05-07 14:10 +0200
Articles 7 — 2 participants

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  Re: foo FTBFS with dh-python >= 3.20180313 Piotr Ożarowski <piotr@debian.org> - 2018-04-26 12:10 +0200
    Re: foo FTBFS with dh-python >= 3.20180313 Andreas Tille <andreas@an3as.eu> - 2018-04-30 14:30 +0200
      Re: foo FTBFS with dh-python >= 3.20180313 Piotr Ożarowski <piotr@debian.org> - 2018-04-30 16:00 +0200
        Re: foo FTBFS with dh-python >= 3.20180313 Andreas Tille <andreas@an3as.eu> - 2018-04-30 20:00 +0200
          Re: foo FTBFS with dh-python >= 3.20180313 Piotr Ożarowski <piotr@debian.org> - 2018-04-30 20:30 +0200
            Re: foo FTBFS with dh-python >= 3.20180313 Andreas Tille <andreas@an3as.eu> - 2018-04-30 23:20 +0200
              How to make sure PATH is set correctly (Was: foo FTBFS with  dh-python >= 3.20180313) Andreas Tille <andreas@an3as.eu> - 2018-05-07 14:10 +0200

#10474 — Re: foo FTBFS with dh-python >= 3.20180313

FromPiotr Ożarowski <piotr@debian.org>
Date2018-04-26 12:10 +0200
SubjectRe: foo FTBFS with dh-python >= 3.20180313
Message-ID<vIM0G-2LO-1@gated-at.bofh.it>
[Andreas Tille, 2018-04-26]
> some packages I maintain received this kind of bug in the case of
> python-skbio it is
> 
>    ModuleNotFoundError: No module named 'skbio'
> 
> So the module that was just build is not found.  I guess this is due to
> some misuse of pybuild - but what did I wrong?  Python-skbio is available
> on Salsa[1] (updated to new upstream but with no change for the current
> problem).
> 
> Any hint how to fix this?

that's because I had to change pybuild's internal paths (to make it work
with multiple modules/packages at the same time).

I added --print option for those who really need it (f.e. while
building sphinx docs) - please use it instead of hardcoding pybuild's
internal paths.

You can use it like this:

 PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) ...


I fixed few packages already, here's a list of other affected ones:

cypari2         Debian Science Team
keras           Debian Science Maintainers
khmer           Debian Med Packaging Team
macs            Debian Med Packaging Team
numba           Debian Science Maintainers
numexpr         Debian Science Maintainers
paleomix        Debian Med Packaging Team
petsc4py        Debian Science Maintainers
pyosmium        Debian GIS Project
pysal           Debian GIS Project
python-gevent   Laszlo Boszormenyi
python-skbio    Debian Med Packaging Team
rows            Paulo Roberto Alves de Oliveira
salt            Debian Salt Team
slepc4py        Debian Science Maintainers
snakemake       Debian Med Packaging Team
statsmodels     Debian Science Maintainers
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#10487

FromAndreas Tille <andreas@an3as.eu>
Date2018-04-30 14:30 +0200
Message-ID<vKg6l-40c-3@gated-at.bofh.it>
In reply to#10474
Hi Piotr,

On Thu, Apr 26, 2018 at 12:01:17PM +0200, Piotr Ożarowski wrote:
> [Andreas Tille, 2018-04-26]
> >    ModuleNotFoundError: No module named 'skbio'
> 
> that's because I had to change pybuild's internal paths (to make it work
> with multiple modules/packages at the same time).
> 
> I added --print option for those who really need it (f.e. while
> building sphinx docs) - please use it instead of hardcoding pybuild's
> internal paths.
> 
> You can use it like this:
> 
>  PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) ...

This worked nicely for python-skbio.
 
> I fixed few packages already, here's a list of other affected ones:
> ...
> snakemake       Debian Med Packaging Team

I tried the same trick for snakemake in Git[1] but failed.

Am I missing something?

Kind regards

       Andreas.


[1] https://salsa.debian.org/med-team/snakemake 

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#10488

FromPiotr Ożarowski <piotr@debian.org>
Date2018-04-30 16:00 +0200
Message-ID<vKhvr-4SV-1@gated-at.bofh.it>
In reply to#10487
[Andreas Tille, 2018-04-30]
> >  PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) ...
> 
> This worked nicely for python-skbio.
>  
> > I fixed few packages already, here's a list of other affected ones:
> > ...
> > snakemake       Debian Med Packaging Team
> 
> I tried the same trick for snakemake in Git[1] but failed.
> 
> Am I missing something?

you changed PYTHONPATH, but PATH still hardcodes old path, I'd start
with that.
-- 
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#10489

FromAndreas Tille <andreas@an3as.eu>
Date2018-04-30 20:00 +0200
Message-ID<vKlfH-7pM-5@gated-at.bofh.it>
In reply to#10488
On Mon, Apr 30, 2018 at 03:57:51PM +0200, Piotr Ożarowski wrote:
> [Andreas Tille, 2018-04-30]
> > >  PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) ...
> > I tried the same trick for snakemake in Git[1] but failed.
> > 
> > Am I missing something?
> 
> you changed PYTHONPATH, but PATH still hardcodes old path, I'd start
> with that.

Hmmm, inside pbuilder chroot the files are installed to

  /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build/bin/snakemake

while

  # pybuild --print build_dir --interpreter python3
  /build/snakemake-4.8.0/.pybuild/cpython3_3.6/build

I have no idea why since some dh-python version things are different
than before but wouldn't it be the best idea to let pybuild set PATH and
PYTHONPATH instead of setting it manually by some manual command?

Kind regards

        Andreas.

-- 
http://fam-tille.de

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#10490

FromPiotr Ożarowski <piotr@debian.org>
Date2018-04-30 20:30 +0200
Message-ID<vKlIK-7Ss-3@gated-at.bofh.it>
In reply to#10489
[Andreas Tille, 2018-04-30]
> On Mon, Apr 30, 2018 at 03:57:51PM +0200, Piotr Ożarowski wrote:
> > [Andreas Tille, 2018-04-30]
> > > >  PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) ...
> > > I tried the same trick for snakemake in Git[1] but failed.
> > > 
> > > Am I missing something?
> > 
> > you changed PYTHONPATH, but PATH still hardcodes old path, I'd start
> > with that.
> 
> Hmmm, inside pbuilder chroot the files are installed to
> 
>   /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build/bin/snakemake
> 
> while
> 
>   # pybuild --print build_dir --interpreter python3
>   /build/snakemake-4.8.0/.pybuild/cpython3_3.6/build

you invoked it outside debian/rules, without --name or PYBUILD_NAME set,
right?

> I have no idea why since some dh-python version things are different
> than before but wouldn't it be the best idea to let pybuild set PATH and
> PYTHONPATH instead of setting it manually by some manual command?

I meant to fix also debian/rules line 11 (you fixed line 21 only)
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#10491

FromAndreas Tille <andreas@an3as.eu>
Date2018-04-30 23:20 +0200
Message-ID<vKonf-1iy-1@gated-at.bofh.it>
In reply to#10490
On Mon, Apr 30, 2018 at 08:29:13PM +0200, Piotr Ożarowski wrote:
> [Andreas Tille, 2018-04-30]
> > Hmmm, inside pbuilder chroot the files are installed to
> > 
> >   /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build/bin/snakemake
> > 
> > while
> > 
> >   # pybuild --print build_dir --interpreter python3
> >   /build/snakemake-4.8.0/.pybuild/cpython3_3.6/build
> 
> you invoked it outside debian/rules, without --name or PYBUILD_NAME set,
> right?

Yes, that's right.
 
> > I have no idea why since some dh-python version things are different
> > than before but wouldn't it be the best idea to let pybuild set PATH and
> > PYTHONPATH instead of setting it manually by some manual command?
> 
> I meant to fix also debian/rules line 11 (you fixed line 21 only)

I commited my last attemt to Git fixing PATH on both lines.

I get with this d/rules:


...
    raise Exception("snakemake not in PATH. For testing, install snakemake with "
Exception: snakemake not in PATH. For testing, install snakemake with 'pip install -e .'. You should do this in a separate environment (via conda or virtualenv).

----------------------------------------------------------------------
Ran 4 tests in 0.187s

FAILED (errors=1)
E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1: cd /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build; python3.6 -m nose tests
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 returned exit code 13
make: *** [debian/rules:17: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
I: copying local configuration
E: Failed autobuilding of package
I: user script /var/cache/pbuilder/build/cow.11501/tmp/hooks/C99_failed_build starting
root:/# echo $PATH
/usr/sbin:/usr/bin:/sbin:/bin


I have no idea why but the PATH does not make it through.

I confirm if I set

   root:/build/snakemake-4.8.0# export PYBUILD_NAME=snakemake
   root:/build/snakemake-4.8.0# pybuild --print build_dir --interpreter python3
   /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build

But why does these variables not end up in the chroot?

Kind regards

       Andreas.

-- 
http://fam-tille.de

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#10503 — How to make sure PATH is set correctly (Was: foo FTBFS with dh-python >= 3.20180313)

FromAndreas Tille <andreas@an3as.eu>
Date2018-05-07 14:10 +0200
SubjectHow to make sure PATH is set correctly (Was: foo FTBFS with dh-python >= 3.20180313)
Message-ID<vMN7Q-11n-5@gated-at.bofh.it>
In reply to#10491
Hi again,

sorry for nagging again but what else than I did in

   https://salsa.debian.org/med-team/snakemake/blob/master/debian/rules

can I do to set PATH in pbuilder.  Possibly I've understand all your
hints incorrectly - the PATH is just not set inside pbuilder chroot. :-(

Kind regards

     Andreas.

On Mon, Apr 30, 2018 at 11:13:44PM +0200, Andreas Tille wrote:
> On Mon, Apr 30, 2018 at 08:29:13PM +0200, Piotr Ożarowski wrote:
> > [Andreas Tille, 2018-04-30]
> > > Hmmm, inside pbuilder chroot the files are installed to
> > > 
> > >   /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build/bin/snakemake
> > > 
> > > while
> > > 
> > >   # pybuild --print build_dir --interpreter python3
> > >   /build/snakemake-4.8.0/.pybuild/cpython3_3.6/build
> > 
> > you invoked it outside debian/rules, without --name or PYBUILD_NAME set,
> > right?
> 
> Yes, that's right.
>  
> > > I have no idea why since some dh-python version things are different
> > > than before but wouldn't it be the best idea to let pybuild set PATH and
> > > PYTHONPATH instead of setting it manually by some manual command?
> > 
> > I meant to fix also debian/rules line 11 (you fixed line 21 only)
> 
> I commited my last attemt to Git fixing PATH on both lines.
> 
> I get with this d/rules:
> 
> 
> ...
>     raise Exception("snakemake not in PATH. For testing, install snakemake with "
> Exception: snakemake not in PATH. For testing, install snakemake with 'pip install -e .'. You should do this in a separate environment (via conda or virtualenv).
> 
> ----------------------------------------------------------------------
> Ran 4 tests in 0.187s
> 
> FAILED (errors=1)
> E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1: cd /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build; python3.6 -m nose tests
> dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 returned exit code 13
> make: *** [debian/rules:17: build] Error 25
> dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
> I: copying local configuration
> E: Failed autobuilding of package
> I: user script /var/cache/pbuilder/build/cow.11501/tmp/hooks/C99_failed_build starting
> root:/# echo $PATH
> /usr/sbin:/usr/bin:/sbin:/bin
> 
> 
> I have no idea why but the PATH does not make it through.
> 
> I confirm if I set
> 
>    root:/build/snakemake-4.8.0# export PYBUILD_NAME=snakemake
>    root:/build/snakemake-4.8.0# pybuild --print build_dir --interpreter python3
>    /build/snakemake-4.8.0/.pybuild/cpython3_3.6_snakemake/build
> 
> But why does these variables not end up in the chroot?
> 
> Kind regards
> 
>        Andreas.
> 
> -- 
> http://fam-tille.de
> 
> 

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