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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
127 stars 35 forks source link

Travis failure for ANTsR/LINDA/LESYMAP ? #313

Closed dorianps closed 4 years ago

dorianps commented 4 years ago

Describe the bug Travis is failing for my downstream packages LESYMAP/LINDA. I am trying to find out why, but the log is not telling much at first glance: https://api.travis-ci.org/v3/job/683673823/log.txt . Looks like ANTsR/Core binaries are being installed but not seen. Looks also like ANTsR has its own problems with failing on Travis.

Any idea how to fix the issues? My travis script relies on http://bit.ly/antsr_travis_sh maintained by @muschellij2.

To Reproduce NA

Expected behavior Travis pass.

Screenshots

Desktop (please complete the following information): NA

Smartphone (please complete the following information): NA

Additional context ANTsR was successful on Travis until 3 weeks ago. Note also, official release version of R is now 4.0.0, not 3.* anymore.

muschellij2 commented 4 years ago

Maybe trusty vs. xenial: https://travis-ci.org/github/dorianps/LESYMAP/jobs/683673823#L9 https://travis-ci.org/github/muschellij2/ANTsR/jobs/682046452#L9

dorianps commented 4 years ago

Both links above are failed builds though. Not sure I follow the logic. Btw, trusty used to be fine for months, these failures have emerged more recently.

stnava commented 4 years ago

recent failures have to do with some work done by @ntustison which requires updated ITK ANTs etc - ie new releases. will get around to eventually.

ntustison commented 4 years ago

I believe I addressed that recent work (simulated displacement fields) when I updated the git tag in ANTsRCore here. Could that be a cache issue?

dorianps commented 4 years ago

Is that affecting the compiled builds used in Travis for downstream packages like lesymap, which seem to be hosted in neuroconductor? Maybe @muschellij2 knows the answer to this.

Installing ANTsRCore package binaries
--2020-05-06 04:11:45--  https://github.com/neuroconductor/ANTsRCore/releases/download/0.7.4.nc4080/ANTsRCore_0.7.4_R_x86_64-pc-linux-gnu_R3.6.tar.gz
Resolving github.com (github.com)... 140.82.112.3
stnava commented 4 years ago

@ntustison did we update the releases? if not then that's one issue ... a 2nd could require cache clearing

ntustison commented 4 years ago

Oh, then yeah, I didn't ever do anything with releases so then that would be a problem.

muschellij2 commented 4 years ago

So it depends on what you're pulling from - either neuroc or the ANTsR repo. If this doesn't work with Neuroc version, then need to update the neuroc version by new submission Best, John

On Thu, May 7, 2020 at 3:15 PM dorianps notifications@github.com wrote:

Is that affecting the compiled builds used in Travis for downstream packages like lesymap, which seem to be hosted in neuroconductor? Maybe @muschellij2 https://github.com/muschellij2 knows the answer to this.

Installing ANTsRCore package binaries --2020-05-06 04:11:45-- https://github.com/neuroconductor/ANTsRCore/releases/download/0.7.4.nc4080/ANTsRCore_0.7.4_R_x86_64-pc-linux-gnu_R3.6.tar.gz Resolving github.com (github.com)... 140.82.112.3

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dorianps commented 4 years ago

@muschellij2 I just rely on your script to get ANTsR/Core on travis before installing lesymap/linda, and that gets the binaries from neurocnductor. It is usually sufficient, but I am always of the idea that the script that installs ANTsR from binaries for travis testing should be a feature ANTsR has itself in the repository. Unfortunately, I can't contribute with something like it anytime soon, just putting out a thought for the other devs.

stnava commented 4 years ago

probably resolved as of the numerous commits this morning --- but still waiting to see

stnava commented 4 years ago

@ntustison @dorianps looks like we are good now re: antsrnet linda etc ... pls close if you agree

dorianps commented 4 years ago

Thanks @stnava . On my packages I still have failures, but it might be because of neuroconductor being behind. Can you please push a commit with the word submit_package_release in it so Neuroconductor picks it up automatically?

ntustison commented 4 years ago

Thanks @stnava. ANTsRNet is now green.

dorianps commented 4 years ago

Had to switch to Xenial for linux to go green, but it works now. Closing.

I suggest someone pushes an empty commit with submit_package_release for neuroconductor to pick up the new release.