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| Started by | Andreas Tille <andreas@an3as.eu> |
|---|---|
| First post | 2018-06-26 12:00 +0200 |
| Last post | 2018-06-27 14:40 +0200 |
| Articles | 4 — 3 participants |
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Bug#894213: No clue yet for building snakemake since there are two dirs in .pybuild Andreas Tille <andreas@an3as.eu> - 2018-06-26 12:00 +0200
Re: No clue yet for building snakemake since there are two dirs in .pybuild Stuart Prescott <stuart@debian.org> - 2018-06-26 18:10 +0200
Re: No clue yet for building snakemake since there are two dirs in .pybuild Piotr Ożarowski <piotr@debian.org> - 2018-06-27 11:10 +0200
Re: No clue yet for building snakemake since there are two dirs in .pybuild Piotr Ożarowski <piotr@debian.org> - 2018-06-27 14:40 +0200
| From | Andreas Tille <andreas@an3as.eu> |
|---|---|
| Date | 2018-06-26 12:00 +0200 |
| Subject | Bug#894213: No clue yet for building snakemake since there are two dirs in .pybuild |
| Message-ID | <w4SVr-7ns-1@gated-at.bofh.it> |
Hi,
meanwhile I upgraded snakemake to latest upstream in Salsa[1]. I keep
on having trouble with building it:
...
Building DAG of jobs...
Using shell: /bin/bash
Job counts:
count jobs
1 1
1
Finished job 0.
1 of 1 steps (100%) done
Complete log: /tmp/tmp3rl_vn12/.snakemake/log/2018-06-26T092103.652823.snakemake.log
.E
======================================================================
ERROR: Failure: 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).)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
raise self.exc_val.with_traceback(self.tb)
File "/usr/lib/python3/dist-packages/nose/loader.py", line 417, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/usr/lib/python3.6/imp.py", line 235, in load_module
return load_source(name, filename, file)
File "/usr/lib/python3.6/imp.py", line 172, in load_source
module = _load(spec)
File "<frozen importlib._bootstrap>", line 684, in _load
File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/build/snakemake-5.1.5/.pybuild/cpython3_3.6_snakemake/build/tests/tests.py", line 22, in <module>
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 0.227s
FAILED (errors=1)
E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1: cd /build/snakemake-5.1.5/.pybuild/cpython3_3.6_snakemake/build; python3.6 -m nose tests
I think the cause of the issue is that there are two dirs in .pybuild:
# ls -l /build/snakemake-5.1.5/.pybuild
total 8
drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6
drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6_snakemake
and the latter contains all the installed files while the former is
empty. How can I prevent this?
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/snakemake
--
http://fam-tille.de
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| From | Stuart Prescott <stuart@debian.org> |
|---|---|
| Date | 2018-06-26 18:10 +0200 |
| Subject | Re: No clue yet for building snakemake since there are two dirs in .pybuild |
| Message-ID | <w4YHv-2wC-3@gated-at.bofh.it> |
| In reply to | #10656 |
Hi Andreas,
>
"/build/snakemake-5.1.5/.pybuild/cpython3_3.6_snakemake/build/tests/tests.py",
> line 22, in <module>
> 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 0.227s
>
> FAILED (errors=1)
> E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1:
> cd /build/snakemake-5.1.5/.pybuild/cpython3_3.6_snakemake/build; python3.6
> -m nose tests
>
>
>
> I think the cause of the issue is that there are two dirs in .pybuild:
>
>
> # ls -l /build/snakemake-5.1.5/.pybuild
> total 8
> drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6
> drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6_snakemake
>
>
> and the latter contains all the installed files while the former is
> empty. How can I prevent this?
Deleting PYBUILD_NAME from your debian/rules is sufficient to fix that. When
set, that sets HOME to the above directory and the build system for some
reason starts using that.
And no, I can't explain why that is...
There are still 3 test failures; the one I glanced at was a missing build-
dep on python3-networkx (and I didn't look further).
cheers
Stuart
--
Stuart Prescott http://www.nanonanonano.net/ stuart@nanonanonano.net
Debian Developer http://www.debian.org/ stuart@debian.org
GPG fingerprint 90E2 D2C1 AD14 6A1B 7EBB 891D BBC1 7EBB 1396 F2F7
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| From | Piotr Ożarowski <piotr@debian.org> |
|---|---|
| Date | 2018-06-27 11:10 +0200 |
| Subject | Re: No clue yet for building snakemake since there are two dirs in .pybuild |
| Message-ID | <w5eCC-3Sb-9@gated-at.bofh.it> |
| In reply to | #10657 |
[Stuart Prescott, 2018-06-26] > > # ls -l /build/snakemake-5.1.5/.pybuild > > total 8 > > drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6 > > drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6_snakemake > > > > and the latter contains all the installed files while the former is > > empty. How can I prevent this? > > Deleting PYBUILD_NAME from your debian/rules is sufficient to fix that. When > set, that sets HOME to the above directory and the build system for some > reason starts using that. > > And no, I can't explain why that is... "cpython3_3.6" is used if --name / PYBUILD_NAME is not defined. Name is added to it to support building multiple modules/extensions at the same time. If snakemake doesn't invoke pybuild twice (with and without --name) then existence of cpython3_3.6 (without "_snakemake") is a bug somewhere in pybuild -- GPG: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645
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| From | Piotr Ożarowski <piotr@debian.org> |
|---|---|
| Date | 2018-06-27 14:40 +0200 |
| Subject | Re: No clue yet for building snakemake since there are two dirs in .pybuild |
| Message-ID | <w5hTP-5Il-1@gated-at.bofh.it> |
| In reply to | #10658 |
[Piotr Ożarowski, 2018-06-27] > [Stuart Prescott, 2018-06-26] > > > # ls -l /build/snakemake-5.1.5/.pybuild > > > total 8 > > > drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6 > > > drwxr-xr-x 3 pbuilder pbuilder 4096 Jun 26 09:20 cpython3_3.6_snakemake > > > > > > and the latter contains all the installed files while the former is > > > empty. How can I prevent this? > > > > Deleting PYBUILD_NAME from your debian/rules is sufficient to fix that. When > > set, that sets HOME to the above directory and the build system for some > > reason starts using that. > > > > And no, I can't explain why that is... > > "cpython3_3.6" is used if --name / PYBUILD_NAME is not defined. Name is > added to it to support building multiple modules/extensions at the same > time. If snakemake doesn't invoke pybuild twice (with and without > --name) then existence of cpython3_3.6 (without "_snakemake") is a bug > somewhere in pybuild FTR: not a bug in pybuild, in line 11 you have: export PATH:=$(shell pybuild --print build_dir --interpreter python3)/bin:$(PATH) and export/pybuild doesn't know about PYBUILD_NAME yet (it's how Makefile works), you need to add "--name $(PYBUILD_NAME)", like this: export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name $(PYBUILD_NAME))/bin:$(PATH) -- GPG: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645
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