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Fix for dplyr 1.0.0 #460

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merged 1 commit into from
Apr 3, 2020
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romainfrancois
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This is 2 fixes that make this package pass against dplyr 1.0.0, this should also work against previous versions of dplyr so don't hesitate to release survminer.

  • This uses group_by() instead of group_by_() which is deprecated
  • This puts the extra "surv_group_by" class first where it is supposed to be instead of last, which messes up with some internal processing from vctrs.

have the extra class first, not last.
@kassambara kassambara merged commit 741ff1e into kassambara:master Apr 3, 2020
@LindaDansereau
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Hello,
Related to this fix I recently used ggsurvplot_facet and got the following warnings in connection with updates to tibble and dplyr. I am using Survminer package v. 0.4.7 and have tried using v.0.4.7.999 as well.

Thank you!

[[1]]

message: as.tibble() is deprecated as of tibble 2.0.0.
Please use as_tibble() instead.
The signature and semantics have changed, see ?as_tibble.
This warning is displayed once every 8 hours.
backtrace:
6. survminer::ggsurvplot_facet(...)
3. survminer::surv_pvalue(...)
3. dplyr::bind_rows(.)
11. tibble::as.tibble(.)

[[2]]

message: select_() is deprecated as of dplyr 0.7.0.
Please use select() instead.
This warning is displayed once every 8 hours.
backtrace:
6. survminer::ggsurvplot_facet(...)
10. dplyr::select_(., .dots = facet.by)
15. dplyr:::lazy_deprec("select", hint = FALSE)

@KaiAragaki
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@LindaDansereau I have noticed the as.tibble message as well and have submitted a PR (#546) to hopefully suppress this particular warning. The select_ -> select conversion will probably take more thought than a simple drop in, I think.

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4 participants