From 3004a2eb786425694d4f590fe03e666c72187f53 Mon Sep 17 00:00:00 2001 From: Raphael Sonabend Date: Tue, 13 Oct 2020 12:36:21 +0100 Subject: [PATCH 01/10] Update tic.yml --- .github/workflows/tic.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/tic.yml b/.github/workflows/tic.yml index e8db005..5ddb0ac 100644 --- a/.github/workflows/tic.yml +++ b/.github/workflows/tic.yml @@ -81,6 +81,10 @@ jobs: Rscript -e "if (!requireNamespace('remotes')) install.packages('remotes', type = 'source')" Rscript -e "if (getRversion() < '3.2' && !requireNamespace('curl')) install.packages('curl', type = 'source')" + - name: "[Custom block] [Stage] [Linux] Install pkgdown system lib req" + if: runner.os == 'Linux' + run: sudo apt install libharfbuzz-dev libfribidi-dev + - name: "[Stage] [Linux] Install curl" if: runner.os == 'Linux' run: sudo apt install libcurl4-openssl-dev From 62842119e4e84a28d5b23720aebd9927f848440d Mon Sep 17 00:00:00 2001 From: Raphael Sonabend Date: Tue, 13 Oct 2020 12:52:14 +0100 Subject: [PATCH 02/10] Update tic.R --- tic.R | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tic.R b/tic.R index 492701d..296d022 100644 --- a/tic.R +++ b/tic.R @@ -5,4 +5,7 @@ if (ci_on_ghactions() && ci_has_env("BUILD_PKGDOWN")) { # creates pkgdown site and pushes to gh-pages branch # only for the runner with the "BUILD_PKGDOWN" env var set do_pkgdown() + + get_stage("deploy") %>% + add_code_step(rmarkdown::render("README.Rmd")) } From 8cd25ae74eabb9c237a8bafb2570654ba261d7ad Mon Sep 17 00:00:00 2001 From: Raphael Sonabend Date: Tue, 13 Oct 2020 15:05:11 +0100 Subject: [PATCH 03/10] Update README.Rmd --- README.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.Rmd b/README.Rmd index ff7b8a4..2fc149e 100644 --- a/README.Rmd +++ b/README.Rmd @@ -24,7 +24,7 @@ set.seed(42) ## What is survivalmodels? -survivalmodels implements models for survival analysis that are either not already implemented in R, or novel implementations for speed improvements. Currently implemented are five neural networks from the Python packages [pycox](https://github.com/havakv/pycox), DNNSurv, +`survivalmodels` implements models for survival analysis that are either not already implemented in R, or novel implementations for speed improvements. Currently implemented are five neural networks from the Python packages [pycox](https://github.com/havakv/pycox), DNNSurv, and the Akritas non-parametric conditional estimator. Further updates will include implementations of noel survival models. ## Installation From 0fc3c84b30d682760375d0c0e127263f4bacc313 Mon Sep 17 00:00:00 2001 From: Raphael Sonabend Date: Tue, 13 Oct 2020 15:54:10 +0100 Subject: [PATCH 04/10] Update tic.R --- tic.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tic.R b/tic.R index 296d022..e03a1ac 100644 --- a/tic.R +++ b/tic.R @@ -2,10 +2,10 @@ do_package_checks() if (ci_on_ghactions() && ci_has_env("BUILD_PKGDOWN")) { + get_stage("deploy") %>% + add_code_step(rmarkdown::render("README.Rmd")) + # creates pkgdown site and pushes to gh-pages branch # only for the runner with the "BUILD_PKGDOWN" env var set do_pkgdown() - - get_stage("deploy") %>% - add_code_step(rmarkdown::render("README.Rmd")) } From 2d5da80d695614fb1599ed48e44337f5dad8e2d4 Mon Sep 17 00:00:00 2001 From: Raphael Sonabend Date: Sat, 17 Oct 2020 09:42:11 +0100 Subject: [PATCH 05/10] Update tic.yml --- .github/workflows/tic.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tic.yml b/.github/workflows/tic.yml index 5ddb0ac..0145530 100644 --- a/.github/workflows/tic.yml +++ b/.github/workflows/tic.yml @@ -81,9 +81,11 @@ jobs: Rscript -e "if (!requireNamespace('remotes')) install.packages('remotes', type = 'source')" Rscript -e "if (getRversion() < '3.2' && !requireNamespace('curl')) install.packages('curl', type = 'source')" - - name: "[Custom block] [Stage] [Linux] Install pkgdown system lib req" + - name: "[Custom block] [Stage] [Linux] Install pkgdown system lib req and valgrind" if: runner.os == 'Linux' - run: sudo apt install libharfbuzz-dev libfribidi-dev + run: | + sudo apt install libharfbuzz-dev libfribidi-dev + sudo apt install -y valgrind - name: "[Stage] [Linux] Install curl" if: runner.os == 'Linux' From 675f56559aad3599b98bd683186b690238bf71a9 Mon Sep 17 00:00:00 2001 From: Raphael Sonabend Date: Wed, 21 Oct 2020 10:32:44 +0100 Subject: [PATCH 06/10] Update tic.R --- tic.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tic.R b/tic.R index e03a1ac..d38073e 100644 --- a/tic.R +++ b/tic.R @@ -3,7 +3,8 @@ do_package_checks() if (ci_on_ghactions() && ci_has_env("BUILD_PKGDOWN")) { get_stage("deploy") %>% - add_code_step(rmarkdown::render("README.Rmd")) + add_code_step(rmarkdown::render("README.Rmd")) %>% + add_step(step_do_push_deploy(commit_paths = c("README.md"))) # creates pkgdown site and pushes to gh-pages branch # only for the runner with the "BUILD_PKGDOWN" env var set From 7cb692f8216b0790f505e44b844520400399c25d Mon Sep 17 00:00:00 2001 From: Raphael Sonabend Date: Wed, 21 Oct 2020 10:33:39 +0100 Subject: [PATCH 07/10] Update README.Rmd --- README.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index 2fc149e..4504d6e 100644 --- a/README.Rmd +++ b/README.Rmd @@ -25,11 +25,11 @@ set.seed(42) ## What is survivalmodels? `survivalmodels` implements models for survival analysis that are either not already implemented in R, or novel implementations for speed improvements. Currently implemented are five neural networks from the Python packages [pycox](https://github.com/havakv/pycox), DNNSurv, -and the Akritas non-parametric conditional estimator. Further updates will include implementations of noel survival models. +and the Akritas non-parametric conditional estimator. Further updates will include implementations of novel survival models. ## Installation -Install the last release from CRAN: +Install the latest release from CRAN: ```{r eval=FALSE} install.packages("survivalmodels") From e73cce99e3ec821024e8c63f9e0e5b5df590b5e9 Mon Sep 17 00:00:00 2001 From: Raphael Sonabend Date: Wed, 21 Oct 2020 11:45:16 +0100 Subject: [PATCH 08/10] Update tic.R --- tic.R | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tic.R b/tic.R index d38073e..e9f2c7d 100644 --- a/tic.R +++ b/tic.R @@ -2,6 +2,10 @@ do_package_checks() if (ci_on_ghactions() && ci_has_env("BUILD_PKGDOWN")) { + +get_stage("before_deploy") %>% + add_step(step_setup_push_deploy(branch = "master", orphan = FALSE)) + get_stage("deploy") %>% add_code_step(rmarkdown::render("README.Rmd")) %>% add_step(step_do_push_deploy(commit_paths = c("README.md"))) From 9cebabd11a96bfd24b1ba4ba05cb116de25390f2 Mon Sep 17 00:00:00 2001 From: GitHub Date: Wed, 21 Oct 2020 10:52:16 +0000 Subject: [PATCH 09/10] Deploy from Github Actions build 319673225 [ci skip] Build URL: https://github.com/RaphaelS1/survivalmodels/actions/runs/319673225 Commit: e73cce99e3ec821024e8c63f9e0e5b5df590b5e9 --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 28748f5..4dbeda0 100644 --- a/README.md +++ b/README.md @@ -20,16 +20,16 @@ MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.or ## What is survivalmodels? -survivalmodels implements models for survival analysis that are either +`survivalmodels` implements models for survival analysis that are either not already implemented in R, or novel implementations for speed improvements. Currently implemented are five neural networks from the Python packages [pycox](https://github.com/havakv/pycox), DNNSurv, and the Akritas non-parametric conditional estimator. Further updates will -include implementations of noel survival models. +include implementations of novel survival models. ## Installation -Install the last release from CRAN: +Install the latest release from CRAN: ``` r install.packages("survivalmodels") From 75fcf5c238d00d9dd8ce7027fc9d1d60a3645747 Mon Sep 17 00:00:00 2001 From: Raphael Sonabend Date: Thu, 22 Oct 2020 10:45:05 +0100 Subject: [PATCH 10/10] Update tic.R --- tic.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tic.R b/tic.R index e9f2c7d..911df29 100644 --- a/tic.R +++ b/tic.R @@ -6,11 +6,11 @@ if (ci_on_ghactions() && ci_has_env("BUILD_PKGDOWN")) { get_stage("before_deploy") %>% add_step(step_setup_push_deploy(branch = "master", orphan = FALSE)) - get_stage("deploy") %>% - add_code_step(rmarkdown::render("README.Rmd")) %>% - add_step(step_do_push_deploy(commit_paths = c("README.md"))) - # creates pkgdown site and pushes to gh-pages branch # only for the runner with the "BUILD_PKGDOWN" env var set do_pkgdown() + + get_stage("deploy") %>% + add_code_step(rmarkdown::render("README.Rmd")) %>% + add_step(step_do_push_deploy(commit_paths = c("README.md"))) }