From 2903d8c5fb8c04dfb40bd7a9f834a7c165c03dc3 Mon Sep 17 00:00:00 2001 From: Daniel Sjoberg Date: Sat, 6 Aug 2022 09:37:24 -0400 Subject: [PATCH 1/3] bump min version of survival --- DESCRIPTION | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 28cff7c6..a0e02252 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -38,7 +38,7 @@ Imports: gtable, kableExtra, rlang (>= 1.0.0), - survival, + survival (>= 3.4-0), tidyr (>= 1.0.0) Suggests: covr, @@ -57,6 +57,7 @@ Suggests: tibble, tidycmprsk (>= 0.1.1), vdiffr +Remotes: therneau/survival VignetteBuilder: knitr biocViews: @@ -64,4 +65,4 @@ Encoding: UTF-8 Language: en-US LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.0 +RoxygenNote: 7.2.1 From f084bd5cac0e448349aeb6407217881e5ba20926 Mon Sep 17 00:00:00 2001 From: Daniel Sjoberg Date: Sat, 6 Aug 2022 09:37:30 -0400 Subject: [PATCH 2/3] Update stat_stepribbon.Rd --- man/stat_stepribbon.Rd | 1 + 1 file changed, 1 insertion(+) diff --git a/man/stat_stepribbon.Rd b/man/stat_stepribbon.Rd index bf233f59..5ac2c57a 100644 --- a/man/stat_stepribbon.Rd +++ b/man/stat_stepribbon.Rd @@ -75,6 +75,7 @@ to the paired geom/stat.} a ggplot } \description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} Provides stair-step values for ribbon plots, often using in conjunction with \code{ggplot2::geom_step()}. The step ribbon can be added with \code{stat_stepribbon()} or From 2100e7b692348d5927c62dd106d4dd60ecd2fb0d Mon Sep 17 00:00:00 2001 From: Daniel Sjoberg Date: Sat, 6 Aug 2022 09:37:38 -0400 Subject: [PATCH 3/3] updated test --- tests/testthat/test-Surv_CNSR.R | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/tests/testthat/test-Surv_CNSR.R b/tests/testthat/test-Surv_CNSR.R index 093af110..0c267833 100644 --- a/tests/testthat/test-Surv_CNSR.R +++ b/tests/testthat/test-Surv_CNSR.R @@ -36,14 +36,7 @@ testthat::test_that("T1.2 The function is compatible with the survival package", testthat::expect_error(survival::survfit(visR::Surv_CNSR(AVAL, CNSR) ~ 1, data = adtte), NA) testthat::expect_error(survival::survfit(visR::Surv_CNSR(AVAL, CNSR) ~ SEX, data = adtte), NA) - # WHEN THIS TEST FAILS, THAT IS OUR SIGNAL THAT {survival} HAS BEEN UPDATED ON CRAN!! - # AT THAT POINT WE SHOULD DO THE FOLLOWING - # 1. UPDATE THIS UNIT TEST TO ASSURE THERE IS _NO_ ERROR WITH coxph() - # 2. ADD A MIN VERSION REQUIREMENT FOR THE {survival} PACKAGE - # THIS CAN BE DONE IN TWO WAYS: - # 1. in the DESCRIPTION file - # 2. using rlang::check_installed("survival", version = ) - testthat::expect_error(survival::coxph(visR::Surv_CNSR() ~ SEX, data = adtte)) + testthat::expect_error(survival::coxph(visR::Surv_CNSR() ~ SEX, data = adtte), NA) })