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basilisk #1318

Closed LTLA closed 4 years ago

LTLA commented 4 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

227f494 Avoid going overboard with escaped backslashes.

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, skipped, TIMEOUT, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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LTLA commented 4 years ago

@grimbough To sum up all of my attempts:

Who knows what's going on here.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

0af546f Protect freeze against PYTHONPATH.

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

0af546f Protect freeze against PYTHONPATH.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

ad8d217 Gave up trying to build this on Windows for the ti...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, TIMEOUT, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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bioc-issue-bot commented 4 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, TIMEOUT, UNSUPPORTED, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

e432732 Re-attempt install on Windows based on how reticul...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

e12174b Try switching entirely to a Miniconda installer on...

bioc-issue-bot commented 4 years ago

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

99d85bb Added dedicated conda setup functions just for Win... b0b1273 Continued propagation of support for condaenvs. fd6b1d5 Streamlined conda setup code and documentation. 0ba8096 Updated calls for env setup in other functions. Ad... e8fb415 Reoxygenated. 3e64aa3 Updated tests for new function calls. c464ef6 Avoid symlinking and directly use base python if p... 423a62f Synchronized non-package location for conda and vi... 5219102 Switched to new env dir, began adding conda tests. b9a17c8 Force the same version of Python in conda envs. e2dccf7 Switched to populating a miniconda install on Wind... 96b0a4a Removed unnecessary test environment variables. 2b6f12d More careful installation of packages to ensure ve... c703527 Reoxygenated. aa0fe58 Updated installation tests and environment setup. 4da9ad4 Switched back to using conda_install. eacfe41 Tested conda environments in basiliskStart. Improv... 04f9ee6 Bugfixes, added missing import. 2788a82 Bugfixes to the onLoad functions. Testfix for basi... 0fae8f4 Bumped version number and date.

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, TIMEOUT, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

734a9b1 Overcome SSL failures for anaconda.

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, TIMEOUT, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

43598c2 Bumped version.

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR, TIMEOUT, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

LTLA commented 4 years ago

Well, @hpages, one easy problem and one hard problem.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

3bbacd4 One more attempt to directly install Anaconda on w...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

hpages commented 4 years ago

Should be a case of restoring the allocated build time to the allowed 40 minutes.

@lshep: How hard would it be to adjust the SPB to support a .BBSoptions option that gives the package some extra time before the TIMEOUT?

Is tokay behind some kind of firewall or proxy server?

Yes it is. But AFAIK this has never caused any sort of SSL issue. In particular Anaconda got downloaded and installed at some point on this machine for the purpose of running the SPB (Single Package Builder).

LTLA commented 4 years ago

In particular Anaconda got downloaded and installed at some point on this machine for the purpose of running the SPB (Single Package Builder).

That's reassuring. So it should be possible.

In any case, the latest build report gets past the installation in build but fails at the next installation attempt within check. That's kind of funny because it's the same set of commands. 30 bucks says that it's a problem with the file path length when slapping the deeply nested Anaconda directories on top of the long path to the temporary R build directory (99 characters by my estimation).

Does the install log (below) offer any insight?

C:/Users/pkgbuild/packagebuilder/workers/jobs/1318/3bbacd4/basilisk.Rcheck/00install.out
lshep commented 4 years ago

Instead of creating a new .BBSoption for this specialized case maybe temporarily flag it as a workflow package that already receives more time? Unless you were planning on implementing a new one on the builders? Adding term Workflow: true to the DESCRIPTION will flag the extra time given to workflows.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

928e650 Pretend we are a workflow package to get extra bui...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

3e315a4 Reorganized internal utilities. 18955fd Divert windows installation to another location.

bioc-issue-bot commented 4 years ago

Dear Package contributor,

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

d719456 Bugfixes for diversion of windows anaconda install...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

e687bd7 Fixed example to avoid conda conflicts.

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

570d379 Try normalizing the path to resolve windows symlin...

bioc-issue-bot commented 4 years ago

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

f04a416 Disabled unnecessary tests on windows.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

170a704 Just give up trying to install this on 32-bit Wind...

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

a4c45ef Update package versions to force environment creat...

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

7cea921 Added package versions to Windows installation dir...

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

1c193de Make sure packageVersion is imported.

bioc-issue-bot commented 4 years ago

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On one or more platforms, the build results were: "WARNINGS, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

30b4fff Coerce backslashes to forward slashes for consiste...

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

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bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

e615a5c More fine-tuning of Windows installation path.

bioc-issue-bot commented 4 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

LTLA commented 4 years ago

YES. YES. YES. AT LAST. (starts crying) I'd like to thank the academy...

The key lesson here seems to be that the Windows path length limit is a nightmare. The temporary build directory path on tokay2 is already long, and stick onto the end the deeply nested Anaconda directories, and BAM, you hit the 260 character limit. This means that, on Windows, we can't install Anaconda into the R installation directory, at least not on the BioC build machines.

To get around this, I've been dumping Anaconda to rappdirs::user_cache_dir() on Windows. This works but I have to name the installation directory by the package version so that it properly re-installs when you re-install basilisk. This means that (i) Windows users have to execute the Anaconda installer on their end and (ii) they will quickly collect multiple 3 GB copies of Anaconda for every bump to basilisk. I don't have a solution for this, and at this point, I don't really care.

You might want to clean out rappdirs::user_cache_dir() on the build machines regularly if this is the solution we'll be using. It doesn't matter to basilisk if the cached installation is destroyed, it'll just re-instantiate it upon package load.

bioc-issue-bot commented 4 years ago

Received a valid push; starting a build. Commits are:

99529fb Provide an option to use an existing Anaconda inst... e3beb4f Simplified handling of pkgname=NULL case for setup... 17f24ea Updated tests for new handling of env install dir. f8bc382 Bugfixes for envdir paths when pkgname=NULL. Strea... 119ff87 Updated vignette. be49a16 Reoxygenated, bumped version and date.