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UCLouvain-CBIO / depmap

Cancer Dependency Map package
https://uclouvain-cbio.github.io/depmap/
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Update depamp for new dplyr release #53

Closed lgatto closed 4 years ago

lgatto commented 4 years ago

This is an automated email to let you know that:

This is a major release. See https://www.tidyverse.org/blog/2020/03/dplyr-1-0-0-is-coming-soon/ for a detailed article about what's changed.

I need your help to keep depmap and dplyr working together smoothly. In the next weeks, can you please:

  1. Read about the changes to dplyr at https://github.com/tidyverse/dplyr/blob/master/NEWS.md. This page includes a list of breaking changes, the reasoning behind them, and to how to update your code.

  2. Carefully inspect the failing checks listed at the bottom of this email.

  3. For each failing check, either update your package, or tell me that I have a bug. If you have made changes to your package, please submit an update to CRAN before May 1.

If you have discovered a bug in dplyr, please file an issue (ideally with a small reprex that illustrates the problem) at https://github.com/tidyverse/dplyr/issues. If you're not sure whether or not you've found a bug, please file an issue at https://github.com/tidyverse/dplyr/issues for discussion. Breaking changes that are not listed qualify as bugs.

Please respond to this message if you have any questions.

tfkillian commented 4 years ago

To clarify: I should install dplyr 1.0 via remotes::install_github("tidyverse/dplyr") and build/check the latest version of depmap and fix all errors and warnings that arise?

lgatto commented 4 years ago

Yes.

tfkillian commented 4 years ago

The Depmap package depends on BiocFileCache, which uses functions select and filter which will be deprecated by dplyr 1.0. An issue has been submitted to their repository, and one of the package maintainers is looking into fixing the code of that package and bringing it in line with the latest version of dplyr.

https://github.com/Bioconductor/BiocFileCache/issues/23

lgatto commented 4 years ago

Do any of the changes to get depmap ready for dplyr 1.0 lead to issues with the current version of dplyr? If not, then please push all the updates now so they can be included in the coming release.

tfkillian commented 4 years ago

The traceback messages from checking the current version of the Depmap package indicate that the only warnings are issued due to use of the BiocFileCache package which uses deprecated functions, and not due to any functions that Depmap currently uses. Therefore, no major changes to Depmap appear necessary (use of BiocFileCache is unavoidable as ExperimentHub depends on it). I have made a 20_Q2 branch and I will push any further changes there. When BiocFileCache is updated to be in line with dplyr 1.0, I will make a new pull request.

lgatto commented 4 years ago

Have you checked the package with the pre-1.0 version of dplyr? If that checks without error/warnings/unexpected notes, please send a PR so that we can push to Bioc before the release.

tfkillian commented 4 years ago

The 20_Q2 branch passes build/check tests for pre-1.0 version of dplyr and a pull request has been made to merge with the master. The version has been bumped to 1.1.3 and the NEWS and DESCRIPTION have been updated accordingly.

lgatto commented 4 years ago

Why is there no metadata_20Q2.csv? Is the 20_Q2 branch really up to date?

tfkillian commented 4 years ago

There is no metadata_20Q2.csv because the 20_Q2 data has not been released yet https://depmap.org/portal/download/. The 20_Q2 branch was intended for updates to be included in the coming release.

lgatto commented 4 years ago

ok