kassambara / survminer

Survival Analysis and Visualization
https://rpkgs.datanovia.com/survminer/
509 stars 164 forks source link

Replace deprecated `tidyr::gather_(...)` in `ggcoxdiagnostics()` #577

Closed jmanitz closed 2 weeks ago

jmanitz commented 2 years ago

The deprecated function tidyr::gather_(...) is used in ggcoxdiagnostics() that needs to be replaced;

> data(cancer, package="survival")
> cph <- coxph(Surv(futime, fustat) ~ rx + age, data=ovarian)
> ggcoxdiagnostics(cph, type="deviance")
`geom_smooth()` using formula 'y ~ x'
Warning message:
`gather_()` was deprecated in tidyr 1.2.0.
Please use `gather()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated. 

> lifecycle::last_lifecycle_warnings()
[[1]]
<deprecated>
message: `gather_()` was deprecated in tidyr 1.2.0.
Please use `gather()` instead.
Backtrace:
 1. survminer::ggcoxdiagnostics(cph, type = "deviance")
 2. tidyr::gather_(...)

session_info()

R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] survminer_0.4.9 ggpubr_0.4.0    ggplot2_3.3.5   survival_3.3-1 

Thanks a lot Juliane

kassambara commented 2 weeks ago

fixed in #579 and #665