Bug#923457: test_likelihood_nh (Failed)
Hi Julien On Tue, Mar 12, 2019 at 11:56:49AM +0100, Julien Y. Dutheil wrote: > Ok, I have committed a patch removing the test. But just realized I did not > update the changelog... should that now be version 2.4.1-3? I've updated d/changelog but will *not* upload anything since meanwhile the package has build on all architectures (randomness was this time on our side) and so there is no need to touch anything. In case the package might receive another RC bug we are now on the safe side. Thanks a lot for your contribution Andreas. -- http://fam-tille.de
Bug#923457: test_likelihood_nh (Failed)
Dear Andreas, Ok, great. Will try to fix that unit test thing upstream for next time. Best, Julien. On Tue, Mar 12, 2019 at 3:18 PM Andreas Tille wrote: > Hi Julien > > On Tue, Mar 12, 2019 at 11:56:49AM +0100, Julien Y. Dutheil wrote: > > Ok, I have committed a patch removing the test. But just realized I did > not > > update the changelog... should that now be version 2.4.1-3? > > I've updated d/changelog but will *not* upload anything since meanwhile > the package has build on all architectures (randomness was this time on > our side) and so there is no need to touch anything. In case the package > might receive another RC bug we are now on the safe side. > > Thanks a lot for your contribution > >Andreas. > > -- > http://fam-tille.de > -- Julien Y. Dutheil, Ph-D 0 (+49) 4522 763 298 § Max Planck Institute for Evolutionary Biology Molecular Systems Evolution Department of Evolutionary Genetics Plön -- GERMANY § Institute of Evolutionary Sciences - Montpellier University of Montpellier 2 -- FRANCE
Bug#923457: test_likelihood_nh (Failed)
On Tue, Mar 12, 2019 at 11:56:49AM +0100, Julien Y. Dutheil wrote: > Dear Andreas, > > Ok, I have committed a patch removing the test. But just realized I did not > update the changelog... should that now be version 2.4.1-3? Thanks, I'll fix the changelog. Andreas. > Cheers, > > Julien. > > On Tue, Mar 12, 2019 at 11:03 AM Andreas Tille wrote: > > > On Tue, Mar 12, 2019 at 09:53:10AM +0100, Julien Y. Dutheil wrote: > > > This all boils down to the fact that this unit test is badly designed: it > > > basically maximizes a function from initial random values. I some > > > particular combinations of initial values though, the convergence may > > fail > > > or take too much time. I will redesign the test, but do not have time at > > > the moment. Would it be possible to just deactivate that test for now? > > > > Sure. IMHO that's the most straightforward way to deal with this issue. > > Since I expect you to be more familiar with the tests I simply assumed > > that you find a more elegant way to deactivate the test than I. ;-) > > > > > In the meantime I also found more symbols errors in libbpp-popgen and I > > > fixed that. I also propagated your modification from bpp-phyl to bpp-seq > > > and bpp-popgen. > > > > I've seen the commits. Thanks for this. I'll upload in case there will > > be more bugs reported. In Freeze we touch only packages with RC bugs. > > > > > On a side note: how can I change my email address (the one that appears > > in > > > the changelog file) ? That one is now deprecated. > > > > It should be changed in debian/control in the Uploaders field as well. > > Both strings need to match each other. > > > > Thanks for your contribution > > > > Andreas. > > > > -- > > http://fam-tille.de > > > > > -- > Julien Y. Dutheil, Ph-D > 0 (+49) 4522 763 298 > > § Max Planck Institute for Evolutionary Biology > Molecular Systems Evolution > Department of Evolutionary Genetics > Plön -- GERMANY > > § Institute of Evolutionary Sciences - Montpellier > University of Montpellier 2 -- FRANCE > ___ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
Bug#923457: test_likelihood_nh (Failed)
Dear Andreas, Ok, I have committed a patch removing the test. But just realized I did not update the changelog... should that now be version 2.4.1-3? Cheers, Julien. On Tue, Mar 12, 2019 at 11:03 AM Andreas Tille wrote: > On Tue, Mar 12, 2019 at 09:53:10AM +0100, Julien Y. Dutheil wrote: > > This all boils down to the fact that this unit test is badly designed: it > > basically maximizes a function from initial random values. I some > > particular combinations of initial values though, the convergence may > fail > > or take too much time. I will redesign the test, but do not have time at > > the moment. Would it be possible to just deactivate that test for now? > > Sure. IMHO that's the most straightforward way to deal with this issue. > Since I expect you to be more familiar with the tests I simply assumed > that you find a more elegant way to deactivate the test than I. ;-) > > > In the meantime I also found more symbols errors in libbpp-popgen and I > > fixed that. I also propagated your modification from bpp-phyl to bpp-seq > > and bpp-popgen. > > I've seen the commits. Thanks for this. I'll upload in case there will > be more bugs reported. In Freeze we touch only packages with RC bugs. > > > On a side note: how can I change my email address (the one that appears > in > > the changelog file) ? That one is now deprecated. > > It should be changed in debian/control in the Uploaders field as well. > Both strings need to match each other. > > Thanks for your contribution > > Andreas. > > -- > http://fam-tille.de > -- Julien Y. Dutheil, Ph-D 0 (+49) 4522 763 298 § Max Planck Institute for Evolutionary Biology Molecular Systems Evolution Department of Evolutionary Genetics Plön -- GERMANY § Institute of Evolutionary Sciences - Montpellier University of Montpellier 2 -- FRANCE
Bug#923457: test_likelihood_nh (Failed)
On Tue, Mar 12, 2019 at 09:53:10AM +0100, Julien Y. Dutheil wrote: > This all boils down to the fact that this unit test is badly designed: it > basically maximizes a function from initial random values. I some > particular combinations of initial values though, the convergence may fail > or take too much time. I will redesign the test, but do not have time at > the moment. Would it be possible to just deactivate that test for now? Sure. IMHO that's the most straightforward way to deal with this issue. Since I expect you to be more familiar with the tests I simply assumed that you find a more elegant way to deactivate the test than I. ;-) > In the meantime I also found more symbols errors in libbpp-popgen and I > fixed that. I also propagated your modification from bpp-phyl to bpp-seq > and bpp-popgen. I've seen the commits. Thanks for this. I'll upload in case there will be more bugs reported. In Freeze we touch only packages with RC bugs. > On a side note: how can I change my email address (the one that appears in > the changelog file) ? That one is now deprecated. It should be changed in debian/control in the Uploaders field as well. Both strings need to match each other. Thanks for your contribution Andreas. -- http://fam-tille.de
Bug#923457: test_likelihood_nh (Failed)
Dear Andreas, This all boils down to the fact that this unit test is badly designed: it basically maximizes a function from initial random values. I some particular combinations of initial values though, the convergence may fail or take too much time. I will redesign the test, but do not have time at the moment. Would it be possible to just deactivate that test for now? In the meantime I also found more symbols errors in libbpp-popgen and I fixed that. I also propagated your modification from bpp-phyl to bpp-seq and bpp-popgen. On a side note: how can I change my email address (the one that appears in the changelog file) ? That one is now deprecated. Best regards, Julien. On Fri, Mar 8, 2019 at 9:36 AM Julien Y. Dutheil wrote: > Dear Andreas, > > Will give it a look asap. > > Best, > > Julien. > > On Fri, Mar 8, 2019 at 9:34 AM Julien Yann Dutheil < > julien.duth...@univ-montp2.fr> wrote: > >> Dear Andreas, >> >> Will give it a look asap. >> >> Best, >> >> Julien. >> >> On Fri, Mar 8, 2019 at 6:30 AM Andreas Tille wrote: >> >>> Hi Julien, >>> >>> after fixing bug #923457 I realised that the package does not >>> build on all architectures[1]. S390x fails with[2] >>> >>> 4/14 Test #5: test_likelihood_nh ...***Failed2.44 sec >>> >>> / 1 >>> - 2 >>> \ 3 >>> - 4 >>> / 5 >>> - 6 >>> \ 7 >>> - 8 >>> / 9 >>> - 10 >>> \ 11 nodes loaded. >>> Theta0 set to 0.444785 >>> Theta1 set to 0.137341 >>> Theta2 set to 0.219281 >>> Theta3 set to 0.759382 >>> Theta4 set to 0.549516 >>> Theta5 set to 0.925583 >>> Theta6 set to 0.527333 >>> Theta7 set to 0.891561 >>> Theta8 set to 0.331932 >>> Theta9 set to 0.523327 >>> Initializing data structure: Done. >>> Number of distinct sites...: 363 >>> Initializing data structure: Done. >>> Number of distinct sites...: 363 >>> >>> Optimizing... / 1 >>> Optimizing... - 2 >>> Optimizing... \ 3 >>> Optimizing... - 4 >>> Optimizing... / 5 >>> Optimizing... - 6 >>> Optimizing... \ 7 >>> Optimizing... - 8 >>> Optimizing... / 9 >>> Optimizing... - 10 >>> Optimizing... \ 11 >>> Optimizing... - 12 >>> Optimizing... / 13 >>> Optimizing... - 14 >>> >>> >>> Optimizing... / 1 >>> Optimizing... - 2 >>> Optimizing... \ 3 >>> Optimizing... - 4 >>> Optimizing... / 5 >>> Optimizing... - 6 >>> Optimizing... \ 7 >>> Optimizing... - 8 >>> Optimizing... / 9 >>> Optimizing... - 10 >>> Optimizing... \ 11 >>> Optimizing... - 12 >>> Optimizing... / 13 >>> Optimizing... - 14 >>> >>> 15: 5347.92 15: 5347.92 >>> 0.516673 0.516673 >>> 0.184681 0.184681 >>> 0.209158 0.209158 >>> 0.795359 0.795359 >>> 0.489372 0.489372 >>> 0.918414 0.918414 >>> 0.489537 0.489537 >>> 0.913968 0.913968 >>> 0.180359 0.180359 >>> 0.797456 0.797456 >>> Initializing data structure: Done. >>> Number of distinct sites...: 365 >>> Initializing data structure: Done. >>> Number of distinct sites...: 365 >>> >>> Optimizing... / 1 >>> Optimizing... - 2 >>> Optimizing... \ 3 >>> Optimizing... - 4 >>> Optimizing... / 5 >>> Optimizing... - 6 >>> Optimizing... \ 7 >>> Optimizing... - 8 >>> Optimizing... / 9 >>> Optimizing... - 10 >>> Optimizing... \ 11 >>> Optimizing... - 12 >>> Optimizing... / 13 >>> Optimizing... - 14 >>> Optimizing... \ 15 >>> Optimizing... - 16 >>> Optimizing... / 17 >>> >>> >>> Optimizing... / 1 >>> Optimizing... - 2 >>> Optimizing... \ 3 >>> Optimizing... - 4 >>> Optimizing... / 5 >>> Optimizing... - 6 >>> Optimizing... \ 7 >>> Optimizing... - 8 >>> Optimizing... / 9 >>> Optimizing... - 10 >>> Optimizing... \ 11 >>> Optimizing... - 12 >>> Optimizing... / 13 >>> Optimizing... - 14 >>> Optimizing... \ 15 >>> Optimizing... - 16 >>> Optimizing... / 17 >>> >>> 18: 5391.43 18: 5391.43 >>> 0.60777 0.60777 >>> 0.127151 0.127151 >>> 0.189039 0.189039 >>> 0.788612 0.788612 >>> 0.564763 0.564763 >>> 0.941319 0.941319 >>> 0.565297 0.565297 >>> 0.844854 0.844854 >>> 0.357532 0.357532 >>> 0.717998 0.717998 >>> Initializing data structure: Done. >>> Number of distinct sites...: 375 >>> Initializing data structure: Done. >>> Number of distinct sites...: 375 >>> >>> Optimizing... / 1 >>> Optimizing... - 2 >>> Optimizing... \ 3 >>> Optimizing... - 4 >>> Optimizing... / 5 >>> Optimizing... - 6 >>> Optimizing... \ 7 >>> Optimizing... - 8 >>> Optimizing... / 9 >>> Optimizing... - 10 >>> Optimizing... \ 11 >>> Optimizing... - 12 >>> Optimizing... / 13 >>> Optimizing... - 14 >>> >>> >>> Optimizing... / 1 >>> Optimizing... - 2 >>> Optimizing... \ 3 >>> Optimizing... - 4 >>> Optimizing... / 5 >>> Optimizing... - 6 >>> Optimizing... \ 7 >>> Optimizing... - 8 >>> Optimizing... / 9 >>> Optimizing... - 10 >>> Optimizing... \ 11 >>> Optimizing... - 12 >>> Optimizing... / 13 >>> Optimizing... - 14 >>> >>> 15: 5401.83 15: 5401.83 >>> 0.419181 0.419181 >>> 0.140299 0.140299 >>> 0.295 0.295 >>> 0.900203 0.900203 >>> 0.411605 0.411605 >>> 0.919716 0.919716 >>> 0.563041 0.563041 >>> 0.813833
Bug#923457: test_likelihood_nh (Failed)
Dear Andreas, Will give it a look asap. Best, Julien. On Fri, Mar 8, 2019 at 9:34 AM Julien Yann Dutheil < julien.duth...@univ-montp2.fr> wrote: > Dear Andreas, > > Will give it a look asap. > > Best, > > Julien. > > On Fri, Mar 8, 2019 at 6:30 AM Andreas Tille wrote: > >> Hi Julien, >> >> after fixing bug #923457 I realised that the package does not >> build on all architectures[1]. S390x fails with[2] >> >> 4/14 Test #5: test_likelihood_nh ...***Failed2.44 sec >> >> / 1 >> - 2 >> \ 3 >> - 4 >> / 5 >> - 6 >> \ 7 >> - 8 >> / 9 >> - 10 >> \ 11 nodes loaded. >> Theta0 set to 0.444785 >> Theta1 set to 0.137341 >> Theta2 set to 0.219281 >> Theta3 set to 0.759382 >> Theta4 set to 0.549516 >> Theta5 set to 0.925583 >> Theta6 set to 0.527333 >> Theta7 set to 0.891561 >> Theta8 set to 0.331932 >> Theta9 set to 0.523327 >> Initializing data structure: Done. >> Number of distinct sites...: 363 >> Initializing data structure: Done. >> Number of distinct sites...: 363 >> >> Optimizing... / 1 >> Optimizing... - 2 >> Optimizing... \ 3 >> Optimizing... - 4 >> Optimizing... / 5 >> Optimizing... - 6 >> Optimizing... \ 7 >> Optimizing... - 8 >> Optimizing... / 9 >> Optimizing... - 10 >> Optimizing... \ 11 >> Optimizing... - 12 >> Optimizing... / 13 >> Optimizing... - 14 >> >> >> Optimizing... / 1 >> Optimizing... - 2 >> Optimizing... \ 3 >> Optimizing... - 4 >> Optimizing... / 5 >> Optimizing... - 6 >> Optimizing... \ 7 >> Optimizing... - 8 >> Optimizing... / 9 >> Optimizing... - 10 >> Optimizing... \ 11 >> Optimizing... - 12 >> Optimizing... / 13 >> Optimizing... - 14 >> >> 15: 5347.92 15: 5347.92 >> 0.516673 0.516673 >> 0.184681 0.184681 >> 0.209158 0.209158 >> 0.795359 0.795359 >> 0.489372 0.489372 >> 0.918414 0.918414 >> 0.489537 0.489537 >> 0.913968 0.913968 >> 0.180359 0.180359 >> 0.797456 0.797456 >> Initializing data structure: Done. >> Number of distinct sites...: 365 >> Initializing data structure: Done. >> Number of distinct sites...: 365 >> >> Optimizing... / 1 >> Optimizing... - 2 >> Optimizing... \ 3 >> Optimizing... - 4 >> Optimizing... / 5 >> Optimizing... - 6 >> Optimizing... \ 7 >> Optimizing... - 8 >> Optimizing... / 9 >> Optimizing... - 10 >> Optimizing... \ 11 >> Optimizing... - 12 >> Optimizing... / 13 >> Optimizing... - 14 >> Optimizing... \ 15 >> Optimizing... - 16 >> Optimizing... / 17 >> >> >> Optimizing... / 1 >> Optimizing... - 2 >> Optimizing... \ 3 >> Optimizing... - 4 >> Optimizing... / 5 >> Optimizing... - 6 >> Optimizing... \ 7 >> Optimizing... - 8 >> Optimizing... / 9 >> Optimizing... - 10 >> Optimizing... \ 11 >> Optimizing... - 12 >> Optimizing... / 13 >> Optimizing... - 14 >> Optimizing... \ 15 >> Optimizing... - 16 >> Optimizing... / 17 >> >> 18: 5391.43 18: 5391.43 >> 0.60777 0.60777 >> 0.127151 0.127151 >> 0.189039 0.189039 >> 0.788612 0.788612 >> 0.564763 0.564763 >> 0.941319 0.941319 >> 0.565297 0.565297 >> 0.844854 0.844854 >> 0.357532 0.357532 >> 0.717998 0.717998 >> Initializing data structure: Done. >> Number of distinct sites...: 375 >> Initializing data structure: Done. >> Number of distinct sites...: 375 >> >> Optimizing... / 1 >> Optimizing... - 2 >> Optimizing... \ 3 >> Optimizing... - 4 >> Optimizing... / 5 >> Optimizing... - 6 >> Optimizing... \ 7 >> Optimizing... - 8 >> Optimizing... / 9 >> Optimizing... - 10 >> Optimizing... \ 11 >> Optimizing... - 12 >> Optimizing... / 13 >> Optimizing... - 14 >> >> >> Optimizing... / 1 >> Optimizing... - 2 >> Optimizing... \ 3 >> Optimizing... - 4 >> Optimizing... / 5 >> Optimizing... - 6 >> Optimizing... \ 7 >> Optimizing... - 8 >> Optimizing... / 9 >> Optimizing... - 10 >> Optimizing... \ 11 >> Optimizing... - 12 >> Optimizing... / 13 >> Optimizing... - 14 >> >> 15: 5401.83 15: 5401.83 >> 0.419181 0.419181 >> 0.140299 0.140299 >> 0.295 0.295 >> 0.900203 0.900203 >> 0.411605 0.411605 >> 0.919716 0.919716 >> 0.563041 0.563041 >> 0.813833 0.813833 >> 0.194868 0.194868 >> 0.801315 0.801315 >> 0.444785 0.514541 0.514541 >> 0.137341 0.15071 0.15071 >> 0.219281 0.231066 0.231066 >> 0.759382 0.828058 0.828058 >> 0.549516 0.48858 0.48858 >> 0.925583 0.926483 0.926483 >> 0.527333 0.539292 0.539292 >> 0.891561 0.857552 0.857552 >> 0.331932 0.244253 0.244253 >> 0.523327 0.772256 0.772256 >> >> >> ... >> >> 93% tests passed, 1 tests failed out of 14 >> >> Total Test time (real) = 31.15 sec >> >> The following tests FAILED: >>5 - test_likelihood_nh (Failed) >> >> >> I remember that I once had even a test failure on my local amd64 - so >> this test might be a bit undetermined. Please confirm this and I'd be >> happy if you could send an *as simple as possible* patch or simply >> deactivate the patch. We are in deep freeze and need to find a quick >> and also simple solution. >> >> Kind regards >> >>Andreas. >> >> >> [1]
Bug#923457: test_likelihood_nh (Failed)
Hi Julien, after fixing bug #923457 I realised that the package does not build on all architectures[1]. S390x fails with[2] 4/14 Test #5: test_likelihood_nh ...***Failed2.44 sec / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 - 8 / 9 - 10 \ 11 nodes loaded. Theta0 set to 0.444785 Theta1 set to 0.137341 Theta2 set to 0.219281 Theta3 set to 0.759382 Theta4 set to 0.549516 Theta5 set to 0.925583 Theta6 set to 0.527333 Theta7 set to 0.891561 Theta8 set to 0.331932 Theta9 set to 0.523327 Initializing data structure: Done. Number of distinct sites...: 363 Initializing data structure: Done. Number of distinct sites...: 363 Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 15: 5347.92 15: 5347.92 0.516673 0.516673 0.184681 0.184681 0.209158 0.209158 0.795359 0.795359 0.489372 0.489372 0.918414 0.918414 0.489537 0.489537 0.913968 0.913968 0.180359 0.180359 0.797456 0.797456 Initializing data structure: Done. Number of distinct sites...: 365 Initializing data structure: Done. Number of distinct sites...: 365 Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 18: 5391.43 18: 5391.43 0.60777 0.60777 0.127151 0.127151 0.189039 0.189039 0.788612 0.788612 0.564763 0.564763 0.941319 0.941319 0.565297 0.565297 0.844854 0.844854 0.357532 0.357532 0.717998 0.717998 Initializing data structure: Done. Number of distinct sites...: 375 Initializing data structure: Done. Number of distinct sites...: 375 Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 15: 5401.83 15: 5401.83 0.419181 0.419181 0.140299 0.140299 0.295 0.295 0.900203 0.900203 0.411605 0.411605 0.919716 0.919716 0.563041 0.563041 0.813833 0.813833 0.194868 0.194868 0.801315 0.801315 0.444785 0.514541 0.514541 0.137341 0.15071 0.15071 0.219281 0.231066 0.231066 0.759382 0.828058 0.828058 0.549516 0.48858 0.48858 0.925583 0.926483 0.926483 0.527333 0.539292 0.539292 0.891561 0.857552 0.857552 0.331932 0.244253 0.244253 0.523327 0.772256 0.772256 ... 93% tests passed, 1 tests failed out of 14 Total Test time (real) = 31.15 sec The following tests FAILED: 5 - test_likelihood_nh (Failed) I remember that I once had even a test failure on my local amd64 - so this test might be a bit undetermined. Please confirm this and I'd be happy if you could send an *as simple as possible* patch or simply deactivate the patch. We are in deep freeze and need to find a quick and also simple solution. Kind regards Andreas. [1] https://buildd.debian.org/status/package.php?p=libbpp-phyl [2] https://buildd.debian.org/status/fetch.php?pkg=libbpp-phyl=s390x=2.4.1-2=1551477555=0 -- http://fam-tille.de
