manually merge develop -> time_varying

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Cyclops
 Type: Package
 Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
-Version: 3.3.1.999
+Version: 3.4.0
 Authors@R: c(
     person("Marc A.", "Suchard", email = "[email protected]", role = c("aut","cre")),
     person("Martijn J.", "Schuemie", role = "aut"),
@@ -52,4 +52,7 @@ Suggests:
     ggplot2,
     microbenchmark,
     cmprsk
+NeedsCompilation: yes
 RoxygenNote: 7.2.3
+Roxygen: list(markdown = TRUE)
+Encoding: UTF-8

NEWS.md

@@ -1,3 +1,10 @@
+develop
+==============
+
+Changes:
+
+1. none yet
+
 Cyclops v3.4.0
 ==============
 

README.md

@@ -1,8 +1,8 @@
 Cyclops
 =======
 
-[![Build Status](https://github.com/ohdsi/Cyclops/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/Cyclops/actions?query=workflow%3AR-CMD-check)
-[![codecov.io](https://app.codecov.io/github/OHDSI/Cyclops/coverage.svg?branch=main)](https://app.codecov.io/github/OHDSI/Cyclops?branch=main)
+[![Build Status](https://github.com/ohdsi/Cyclops/actions/workflows/R_CMD_check_Hades.yaml/badge.svg)](https://github.com/OHDSI/Cyclops/actions?query=workflow%3AR-CMD-check)
+[![codecov.io](https://codecov.io/github/OHDSI/Cyclops/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Cyclops?branch=main)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/Cyclops)](https://CRAN.R-project.org/package=Cyclops)
 [![CRAN_Status_Badge](https://cranlogs.r-pkg.org/badges/Cyclops)](https://cran.r-project.org/package=Cyclops)
 

cran-comments.md

@@ -1,16 +1,9 @@
-## Resubmission after VALGRIND feedback from Brian Ripley
+## Submission of v3.4.0
 
-* fixed VALGRIND uninitialized value (UB) issue; variable 'priorType' was uninitialized,
-  specifically in:
-
-    ==2293460== Conditional jump or move depends on uninitialised value(s)
-    ==2293460==    at 0x22CE4848: bsccs::CyclicCoordinateDescent::computeAsymptoticPrecisionMatrix() (packages/tests-vg/Cyclops/src/cyclops/CyclicCoordinateDescent.cpp:1335)
+* fixed use of deprecated `$` function in `dbplyr` using CRAN errors
 
-* fixed VALGRIND memory leak issue; was caused by calls to '::Rf_error()' instead of 
-  'Rcpp::stop()' when handling some error edge-cases
-
 ## Test environments
-* local OS X install, R 4.1
+* local OS X install, R 4.3
 * r-devel-valgrind docker container
 * ubuntu 20.04 (via gh-actions: devel and release)
 * win-builder (devel and release)