Update depamp for new dplyr release about depmap

[tfkillian]

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]

Yes.

[tfkillian]

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.

Bioconductor/BiocFileCache#23

[lgatto]

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]

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]

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]

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]

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

[tfkillian]

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]

ok