Bug#878498: snakemake FTBFS with Python 3.6 as default
On Mon, Dec 11, 2017 at 03:45:50PM +0100, Andreas Tille wrote: > > Will let you know when I'm through with those and all is pushed to > > alioth again. The current master passes build in a cowbuilder that has access to python3-ratelimiter, and lintian's only serious complaints are the privacy violations (JavsScript and badges in the documentation and some web application templates -- Snakemake has a web application?) that have been there in the old release too and I don't have a plan on how to fix them yet. The new test suite system patch-outs are for * r-cran-rmarkdown (filed as #884115, thanks Andreas for ITP-ing), and * google-cloud-sdk (quoting the patch description: Whether this needs a Debian RFP or should be forwarded is undecided yet given I have no clue about what those Google Cloud SDK actually does). IMO that package state is an enhancement over the last one in the archive and can be considered for upload, if one is willing to accept the abovementioned lintian warnings. Best regards Christian -- To use raw power is to make yourself infinitely vulnerable to greater powers. -- Bene Gesserit axiom signature.asc Description: PGP signature
Bug#878498: snakemake FTBFS with Python 3.6 as default
On Mon, Dec 11, 2017 at 03:35:53PM +0100, chrysn wrote: > I've got them all down locally; it'll need some cleaning up (and > possibly upstreaming) of patches, and I have yet to run it in a pbuilder > to see which build dependencies popped up that are undeclared so far, > but I don't expect any showstoppers there. > > Will let you know when I'm through with those and all is pushed to > alioth again. Thanks a lot - that's very helpful Andreas. -- http://fam-tille.de
Bug#878498: snakemake FTBFS with Python 3.6 as default
> The problem is that when trying to build this I get a lot of errors in > the build time tests. Is there any volunteer to have a look? I've got them all down locally; it'll need some cleaning up (and possibly upstreaming) of patches, and I have yet to run it in a pbuilder to see which build dependencies popped up that are undeclared so far, but I don't expect any showstoppers there. Will let you know when I'm through with those and all is pushed to alioth again. Best regards chrysn -- To use raw power is to make yourself infinitely vulnerable to greater powers. -- Bene Gesserit axiom signature.asc Description: PGP signature
Bug#878498: snakemake FTBFS with Python 3.6 as default
On Fri, Dec 08, 2017 at 09:18:42AM +0100, Andreas Tille wrote: > The problem is that when trying to build this I get a lot of errors in > the build time tests. Is there any volunteer to have a look? I've started with the tests more or less at random, and the second seems to be promising to solve most of them: * test_delete_output is IMO an upstream bug that only triggers when SHELL does not try to be POSIX compatible (why should it unless invoked as `sh`), eg. when SHELL=zsh. There are 3 more that fail even when run locally w/o any Debian modifications, so we might need to mask them or apply any of the workarounds. (Postponed that until the big ones are done). * The noop-rate-limiter workaround I introduced earlier to be able to work on the other issues of the new version doesn't work right now. Before I spend any more time fixing a workaround, I'll go ahead and ITP python3-ratelimiter [880661] -- with that workaround in place, we shouldn't release an updated snakemake anyway. If the delay introduced by ratelimiter (even with me getting packaging done "immediately" and follow-up sponsorship from DPMT, this will need to go through NEW. Best regards chrysn [1]: https://bitbucket.org/snakemake/snakemake/issues/722/tests-fail-when-shell-is-zsh-and-not-bash [880661]: https://bugs.debian.org/880661 -- To use raw power is to make yourself infinitely vulnerable to greater powers. -- Bene Gesserit axiom signature.asc Description: PGP signature
Bug#878498: snakemake FTBFS with Python 3.6 as default
Hi, On Thu, Dec 07, 2017 at 10:49:57AM +0500, Andrey Rahmatullin wrote: > > I've upgraded snakemake in Git to latest upstream but its featuring the > > same issue. I'm pretty sure you Python people know a simple answer for > > this issue. > Did you see this part? > > > > The problem is the the following line in debian/rules: > > > > > > export PATH:=$(CURDIR)/.pybuild/pythonX.Y_3.5/build/bin:$(PATH) I can confirm that after Andrey read this part aloud to me the patch was really simple. So what we could do is uploading the current old version of snakemake to fix this bug. However Chris has pointed out to me that we are lagging behind upstream and injected a new upstream version. Meanwhile there was another version bump and I imported the latest version (Chris, please make sure you also import pristine-tar next time). The problem is that when trying to build this I get a lot of errors in the build time tests. Is there any volunteer to have a look? Kind regards Andreas. -- http://fam-tille.de
Bug#878498: snakemake FTBFS with Python 3.6 as default
On Wed, Dec 06, 2017 at 10:14:45PM +0100, Andreas Tille wrote: > control: tags -1 help > > Hi, > > I've upgraded snakemake in Git to latest upstream but its featuring the > same issue. I'm pretty sure you Python people know a simple answer for > this issue. Did you see this part? > > The problem is the the following line in debian/rules: > > > > export PATH:=$(CURDIR)/.pybuild/pythonX.Y_3.5/build/bin:$(PATH) -- WBR, wRAR signature.asc Description: PGP signature
Processed: Re: Bug#878498: snakemake FTBFS with Python 3.6 as default
Processing control commands: > tags -1 help Bug #878498 [src:snakemake] snakemake FTBFS with Python 3.6 as default Added tag(s) help. -- 878498: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=878498 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
Bug#878498: snakemake FTBFS with Python 3.6 as default
control: tags -1 help
Hi,
I've upgraded snakemake in Git to latest upstream but its featuring the
same issue. I'm pretty sure you Python people know a simple answer for
this issue.
Any help would be welcome
Andreas.
On Sat, Oct 14, 2017 at 05:33:22AM +0300, Adrian Bunk wrote:
> Source: snakemake
> Version: 3.10.0-1
> Severity: serious
> Tags: buster sid
>
> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/snakemake.html
>
> ...
> ==
> 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 418, 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 "", line 684, in _load
> File "", line 665, in _load_unlocked
> File "", line 678, in exec_module
> File "", line 219, in _call_with_frames_removed
> File
> "/build/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/build/tests/tests.py",
> line 21, in
> 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 0.535s
>
> FAILED (errors=1)
> E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd
> /build/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose
> tests
> dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 returned
> exit code 13
> debian/rules:18: recipe for target 'build' failed
> make: *** [build] Error 25
>
>
>
> The problem is the the following line in debian/rules:
>
> export PATH:=$(CURDIR)/.pybuild/pythonX.Y_3.5/build/bin:$(PATH)
>
> ___
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> debian-med-packag...@lists.alioth.debian.org
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>
--
http://fam-tille.de
Bug#878498: snakemake FTBFS with Python 3.6 as default
On Sun, Dec 03, 2017 at 06:47:48PM +0100, Andreas Tille wrote: > Ping? sorry, I thought I had already done that: my latest WIP state is now pushed; it includes a patch that disables rate limiting for sake of being able to work on the main issue, but I haven't made any progress there yet. signature.asc Description: PGP signature
Bug#878498: snakemake FTBFS with Python 3.6 as default
Ping? On Sat, Nov 11, 2017 at 09:43:58AM +0100, Andreas Tille wrote: > Hi Chrysn, > > since nobody raised any veto and we finally will follow upstream anyway: > Could you please push your changes to latest upstream version and than > we try to work together from there? For instance it will help to contact > upstream when refering to the latest upstream version. -- http://fam-tille.de
Bug#878498: snakemake FTBFS with Python 3.6 as default
Hi Chrysn, since nobody raised any veto and we finally will follow upstream anyway: Could you please push your changes to latest upstream version and than we try to work together from there? For instance it will help to contact upstream when refering to the latest upstream version. Kind regards Andreas. -- http://fam-tille.de
Bug#878498: snakemake FTBFS with Python 3.6 as default
Package: src:snakemake Followup-For: Bug #878498 The test also fails with the 3.13.3 version in the team repository. I've had a short look at whether upgrading to 4.3.0 helps (minimal patch refreshing and new build dependency on python3-configargparse as well as the unpackaged ratelimiter module), but the same condition shows up there as well. I'll probably need to fix this, but as I'm new to snakemake: Will this need keeping the 3 version around, or can I just go ahead and proceed with 4.3.0? Best regards chrysn -- System Information: Debian Release: buster/sid APT prefers unstable-debug APT policy: (500, 'unstable-debug'), (500, 'unstable'), (1, 'experimental-debug'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 4.14.0-rc7-amd64 (SMP w/4 CPU cores) Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB:en (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) -- To use raw power is to make yourself infinitely vulnerable to greater powers. -- Bene Gesserit axiom signature.asc Description: PGP signature
Bug#878498: snakemake FTBFS with Python 3.6 as default
Source: snakemake
Version: 3.10.0-1
Severity: serious
Tags: buster sid
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/snakemake.html
...
==
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 418, 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 "", line 684, in _load
File "", line 665, in _load_unlocked
File "", line 678, in exec_module
File "", line 219, in _call_with_frames_removed
File
"/build/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/build/tests/tests.py", line
21, in
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 0.535s
FAILED (errors=1)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd
/build/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose
tests
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 returned
exit code 13
debian/rules:18: recipe for target 'build' failed
make: *** [build] Error 25
The problem is the the following line in debian/rules:
export PATH:=$(CURDIR)/.pybuild/pythonX.Y_3.5/build/bin:$(PATH)
