fix space issue and set seed

sahirbhatnagar · Apr 9, 2024 · 96a64b1 · 96a64b1
1 parent 1bee7f2
commit 96a64b1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: casebase
 Type: Package
 Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression
-Version: 0.10.4
-Date: 2024-02-01
+Version: 0.10.5
+Date: 2024-04-09
 Authors@R: 
     c(person(given = "Sahir",
              family = "Bhatnagar",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# casebase 0.10.5
+
+* Skip tests when R is compiled against ATLAS BLAS
+* Set seed for reproducible tests
+
 # casebase 0.10.4
 
 * Fix bug with tangled outputs of vignettes.

diff --git a/tests/testthat/test-absRisk.R b/tests/testthat/test-absRisk.R
@@ -1,6 +1,9 @@
 context("Absolute risk")
+set.seed(12345)
+
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 # Handling warning messages coming from montecarlo integration
 handler_validmc <- function(msg) {

diff --git a/tests/testthat/test-absRiskComp.R b/tests/testthat/test-absRiskComp.R
@@ -1,6 +1,9 @@
 context("Absolute risk-Comp risk")
+set.seed(12345)
+
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 # Handling warning messages coming from montecarlo integration
 handler_validmc <- function(msg) {

diff --git a/tests/testthat/test-confint.R b/tests/testthat/test-confint.R
@@ -1,3 +1,10 @@
+context("Confidence intervals")
+set.seed(12345)
+
+# CRAN skip atlas check fix
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
+
 # Handling warning messages coming from montecarlo integration
 handler_validmc <- function(msg) {
     if (any(grepl("out of range", msg))) invokeRestart("muffleWarning")

diff --git a/tests/testthat/test-fitting.R b/tests/testthat/test-fitting.R
@@ -1,6 +1,9 @@
 context("Fitting")
+set.seed(12345)
+
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 
 n <- 100

diff --git a/tests/testthat/test-fittingComp.R b/tests/testthat/test-fittingComp.R
@@ -1,6 +1,9 @@
 context("Fitting-Comp risk")
+set.seed(12345)
+
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 
 n <- 100

diff --git a/tests/testthat/test-gam.R b/tests/testthat/test-gam.R
@@ -1,6 +1,9 @@
 context("GAMs")
+set.seed(12345)
+
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 # Skip tests if mgcv is not installed
 testthat::skip_if_not_installed("mgcv")

diff --git a/tests/testthat/test-gbm.R b/tests/testthat/test-gbm.R
@@ -1,6 +1,11 @@
 context("GBMs")
+set.seed(12345)
+
+testthat::skip_if(TRUE, message = 'GBM is not implemented')
+
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 # Skip tests if gbm is not installed
 testthat::skip_if_not_installed("gbm")

diff --git a/tests/testthat/test-glmnet.R b/tests/testthat/test-glmnet.R
@@ -1,7 +1,9 @@
 context("glmnet")
+set.seed(12345)
 
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 # Skip tests if gbm is not installed
 testthat::skip_if_not_installed("glmnet")

diff --git a/tests/testthat/test-matrix.R b/tests/testthat/test-matrix.R
@@ -1,7 +1,9 @@
 context("Matrix interface")
-# CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+set.seed(12345)
 
+# CRAN skip atlas check fix
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 N <- 1000; p <- 30
 nzc <- 0.33 * p

diff --git a/tests/testthat/test-plotHazard.R b/tests/testthat/test-plotHazard.R
@@ -1,6 +1,9 @@
 context("plotHazard")
+set.seed(12345)
+
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 skip_if_not_installed("glmnet")
 skip_if_not_installed("mgcv")

diff --git a/tests/testthat/test-plotSingleEventCB.R b/tests/testthat/test-plotSingleEventCB.R
@@ -1,7 +1,9 @@
 context("plot.singleEventCB")
+set.seed(12345)
 
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 # Uncomment next line to skip tests in non-interactive session
 skip_if_not_installed("glmnet")

diff --git a/tests/testthat/test-plotabsRiskCB.R b/tests/testthat/test-plotabsRiskCB.R
@@ -1,7 +1,9 @@
 context("Absolute risk plotting")
+set.seed(12345)
 
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 # Handling warning messages coming from montecarlo integration
 handler_validmc <- function(msg) {

diff --git a/tests/testthat/test-popTime.R b/tests/testthat/test-popTime.R
@@ -1,7 +1,9 @@
 context("popTime methods")
+set.seed(12345)
 
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 nobs <- 500
 

diff --git a/tests/testthat/test-sampling.R b/tests/testthat/test-sampling.R
@@ -1,7 +1,9 @@
 context("Sampling")
+set.seed(12345)
 
 # CRAN skip atlas check fix
-testthat::skip_if(grepl(pattern = "atlas",sessionInfo()$BLAS,ignore.case=TRUE))
+testthat::skip_if(grepl(pattern = "atlas", sessionInfo()$BLAS,
+                        ignore.case = TRUE))
 
 # Create simulated data with competing risks----
 nobs <- 500