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knausb / vcfR

Tools to work with variant call format files
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fix #160 #161

Closed jan-glx closed 4 years ago

jan-glx commented 4 years ago

This fixes #160.

coveralls commented 4 years ago

Coverage Status

Coverage remained the same at 67.486% when pulling 9fb4557e06a86d9f5431b4bb0c9de3d0202ede69 on jan-glx:patch-1 into 6c2b1d36f4a0f4e475ba1a25c368b74eb139e59b on knausb:master.

jan-glx commented 4 years ago

Appveyor ran through too now (thanks to 9fb4557 allowing source dependencies), remaining CI errors are unrelated warnings from a bad link in the documentation:

* checking Rd cross-references ... WARNING
Non-file package-anchored link(s) in documentation object 'chromR-class.Rd':
  '[base]{tolower}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

Hope this helps, let me know if I should change anything - Jan

knausb commented 4 years ago

The suggestion to remove configure was raised and addressed in other issues. Modification of the appveyor yaml should only affect appveyor, so I don't see why it's necessary. Appveyor failed for your PR but I'm guessing it has to do with dependencies still being sorted out from the major release of R 4.0.0.

Thank you @jan-glx for proposing a solution! Brian

jan-glx commented 4 years ago

Great to hear that you fixed #160 yourself now (with b59851027 and 55aed8f8d18f7d867f7)! 🎉 I included 9fb4557 in this PR such that appvoyer will also consider source packages when installing dependencies and thus be able to check my changes. You might want to consider merging / cherry picking 9fb4557 nevertheless to enable CI for windows again (in my experience there are always some packages that require compilation on windows). (Or do you really want to check that windows users don't need build tools to use vcfr?)

knausb commented 4 years ago

Hi @jan-glx ,

It appears that I did not understand what PKGTYPE: both did. And now I do. It appears we've gone full circle in that I did not accept your PR but have now incorporated all of your proposals. We seem to have landed at "you understood this better than I did from the beginning." Apologies, you're working with a human here. Thank you for proposing solutions! And thank you for being persistent!

Brian

jan-glx commented 4 years ago

Very human response. Much appreciated!