manually merge gpu_cox -> time_varying

OHDSI · Oct 20, 2023 · 7538e27 · 7538e27
2 parents fee07f5 + d8ceec2
commit 7538e27
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -34,3 +34,7 @@ deprecated
 ^\.github$
 ^CRAN-RELEASE$
 .covrignore
+src/Makevars$
+src/Makevars.win$
+to_fix*
+^CRAN-SUBMISSION$
diff --git a/.gitignore b/.gitignore
@@ -35,3 +35,5 @@ CRAN-RELEASE
 .DS_Store
 *.gcno
 *.gcda
+src/Makevars
+src/Makevars.win
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 3.3.1
+Date: 2023-04-09 20:06:33 UTC
+SHA: d88c531efa06933c1007cb785343f1382c95ee0d
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Cyclops
 Type: Package
 Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
-Version: 3.2.1
+Version: 3.3.1.99
 Authors@R: c(
     person("Marc A.", "Suchard", email = "msuchard@ucla.edu", role = c("aut","cre")),
     person("Martijn J.", "Schuemie", role = "aut"),
@@ -26,6 +26,7 @@ Description: This model fitting tool incorporates cyclic coordinate descent and
     Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.
 License: Apache License 2.0
 LazyData: Yes
+Biarch: true
 URL: https://github.com/ohdsi/cyclops
 BugReports: https://github.com/ohdsi/cyclops/issues
 Depends:
@@ -51,4 +52,4 @@ Suggests:
     ggplot2,
     microbenchmark,
     cmprsk
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
diff --git a/NEWS.md b/NEWS.md
@@ -4,7 +4,26 @@ develop
 Changes:
 
 1. improvements on adaptive likelihood profiling
+2. add `auto` option to `cvRepetitions`
+3. bumped explicit C++11 requirement up to R v4.1
 
+Cyclops v3.3.1
+==============
+
+Changes:
+
+1. fix uninitialized value in detected in computeAsymptoticPrecisionMatrix(); value was priorType
+2. fix memory leak caused by call to ::Rf_error()
+3. fix line-endings on Makevar on windows
+
+Cyclops v3.3.0
+==============
+
+1. bump for R 4.2
+2. fix CRAN warnings
+    a. used `minValues`
+3. fix CRAN notes
+    a. remove explicit dependence on C++11 (except for R <= 4.0)   
 
 Cyclops v3.2.1
 ==============
@@ -14,6 +33,7 @@ Changes:
 1. fix small memory leak caused by direct call to '::Rf_error()'
 2. disable JVM calls on CRAN due to uninitialized memory in Java JVM
 
+
 Cyclops v3.2.0
 ==============
 

diff --git a/R/Cyclops-package.R b/R/Cyclops-package.R
@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL
diff --git a/R/ModelFit.R b/R/ModelFit.R
@@ -204,6 +204,11 @@ fitCyclopsModel <- function(cyclopsData,
             writeLines(paste("Using cross-validation selector type", control$selectorType))
         }
     }
+
+    if (control$cvRepetitions == "auto") {
+        control$cvRepetitions <- .getNumberOfRepetitions(getNumberOfRows(cyclopsData))
+    }
+
     control <- .setControl(cyclopsData$cyclopsInterfacePtr, control)
     threads <- control$threads
 
@@ -218,6 +223,7 @@ fitCyclopsModel <- function(cyclopsData,
         }
 
         .cyclopsSetBeta(cyclopsData$cyclopsInterfacePtr, startingCoefficients)
+        .cyclopsSetStartingBeta(cyclopsData$cyclopsInterfacePtr, startingCoefficients)
     }
 
     if (!is.null(fixedCoefficients)) {
@@ -324,6 +330,11 @@ fitCyclopsModel <- function(cyclopsData,
     fit$scale <- cyclopsData$scale
     fit$threads <- threads
     fit$seed <- control$seed
+
+    if (prior$useCrossValidation) {
+        fit$cvRepetitions <- control$cvRepetitions
+    }
+
     class(fit) <- "cyclopsFit"
     return(fit)
 }
@@ -784,7 +795,6 @@ getSEs <- function(object, covariates) {
     ses
 }
 
-
 #' @title Run Bootstrap for Cyclops model parameter
 #'
 #' @param object    A fitted Cyclops model object
@@ -1136,3 +1146,11 @@ convertToGlmnetLambda <- function(variance, nobs) {
     graph <-  lapply(0:(nParents - 1), function(n, types) { 0:(nTypes - 1) + n * nTypes }, types = nTypes)
     graph
 }
+
+.getNumberOfRepetitions <- function(nrows) {
+    top <- 1E2
+    factor <- 0.5
+    pmax(pmin(
+        ceiling(top / nrows^(factor))
+        , 10), 1)
+}
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -25,10 +25,22 @@
     invisible(.Call(`_Cyclops_cyclopsSetBeta`, inRcppCcdInterface, beta))
 }
 
+.cyclopsGetBeta <- function(inRcppCcdInterface, index) {
+    .Call(`_Cyclops_cyclopsGetBeta`, inRcppCcdInterface, index)
+}
+
+.cyclopsSetStartingBeta <- function(inRcppCcdInterface, inStartingBeta) {
+    invisible(.Call(`_Cyclops_cyclopsSetStartingBeta`, inRcppCcdInterface, inStartingBeta))
+}
+
 .cyclopsSetFixedBeta <- function(inRcppCcdInterface, beta, fixed) {
     invisible(.Call(`_Cyclops_cyclopsSetFixedBeta`, inRcppCcdInterface, beta, fixed))
 }
 
+.cyclopsGetFixedBeta <- function(inRcppCcdInterface, index) {
+    .Call(`_Cyclops_cyclopsGetFixedBeta`, inRcppCcdInterface, index)
+}
+
 .cyclopsGetIsRegularized <- function(inRcppCcdInterface, index) {
     .Call(`_Cyclops_cyclopsGetIsRegularized`, inRcppCcdInterface, index)
 }

diff --git a/R/Survfit.R b/R/Survfit.R
@@ -4,15 +4,17 @@
 #' @description
 #' \code{survfit.cyclopsFit} computes baseline hazard function
 #'
-#' @param cyclopsFit A Cyclops survival model fit object
+#' @param formula A Cyclops survival model fit object
 #' @param type type of baseline survival, choices are: "aalen" (Breslow)
+#' @param ... for future methods
 #'
 #' @return Baseline survival function for mean covariates
 #'
 #' @importFrom survival survfit
 #'
 #' @export
-survfit.cyclopsFit <- function(cyclopsFit, type="aalen") {
+survfit.cyclopsFit <- function(formula, type="aalen", ...) {
+    cyclopsFit <- formula
     delta = meanLinearPredictor(cyclopsFit)
 
     times = getTimeVector(cyclopsFit$cyclopsData)

diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@ 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://codecov.io/github/OHDSI/Cyclops/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Cyclops?branch=main)
+[![codecov.io](https://app.codecov.io/github/OHDSI/Cyclops/coverage.svg?branch=main)](https://app.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)
 
@@ -76,7 +76,7 @@ License
 =======
 Cyclops is licensed under Apache License 2.0.   Cyclops contains the TinyThread libray.
 
-The TinyThread library is licensed under the [zlib/libpng](https://opensource.org/licenses/Zlib/) license as described [here](https://tinythreadpp.bitsnbites.eu/).
+The TinyThread library is licensed under the [zlib/libpng](https://opensource.org/license/zlib-license-php/) license as described [here](https://tinythreadpp.bitsnbites.eu/).
 
 Development
 ===========

diff --git a/cleanup b/cleanup
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+rm -f config.* src/Makevars src/Markvars.win src/config.h
diff --git a/configure b/configure
@@ -0,0 +1,18 @@
+#!/usr/bin/env sh
+
+# adapted from https://github.com/tidyverse/purrr/blob/main/configure
+
+# Check that this is not just ./configure. We need to run this
+# from R CMD INSTALL, to have the R env vars set.
+
+if [ -z "$R_HOME" ]; then
+echo >&2 R_HOME is not set, are you running R CMD INSTALL?
+exit 1
+fi
+
+# Find the R binary we need to use. This is a bit trickier on
+# Windows, because it has two architectures. On windows R_ARCH_BIN
+# is set, so this should work everywhere.
+RBIN="${R_HOME}/bin${R_ARCH_BIN}/R"
+
+"$RBIN" --vanilla --slave -f tools/configure.R
diff --git a/configure.win b/configure.win
@@ -0,0 +1,2 @@
+#! /usr/bin/env sh
+sh ./configure
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,30 +1,24 @@
-## Re-submission after 'valgrind' check email from Uwe Ligges:
+## Resubmission after VALGRIND feedback from Brian Ripley
 
-```
-Thanks, we see with valgrind it is better, but still leaking. 
-```
+* fixed VALGRIND uninitialized value (UB) issue; variable 'priorType' was uninitialized,
+  specifically in:
 
-## Fixes
-
-* all definite leaks on my M1 and linux (R 4.1) valgrind-versions are now gone.
-* replaced calls to '::Rf_error()' with 'Rcpp::stop()' to ensure that destructors get 
-  called before returning to R.
-* removed calls to JVM through Andromeda package (was an issue with the CRAN system JVM).
+    ==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 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
+* r-devel-valgrind docker container
 * ubuntu 20.04 (via gh-actions: devel and release)
 * win-builder (devel and release)
 
 ## R CMD check results
-* There were no ERRORs
-* There is 1 occasional WARNING:
-  inclusion of 'abort'.
-
-This inclusion comes from 'RcppEigen' and not 'Cyclops' on some platforms with R-devel.  
-
+* There were no ERRORs or WARNINGs   
 * There is 1 occasional NOTE:
-  checking installed package size ... NOTE
+    checking installed package size ... NOTE
     installed size is 22.5Mb
     sub-directories of 1Mb or more:
       libs 21.7Mb
@@ -37,3 +31,5 @@ availability of C++17 'if (constexpr ...)' should decrease library size substant
 ## Downstream dependencies
 * 'EvidenceSynthesis' - checked and works.
 * 'EmpiricalCalibration' - checked and works.
+* 'IterativeHardThresholding' - checked and works.
+* 'BrokenAdaptiveRidge' - checked and works.
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,11 +1,11 @@
 citHeader("To cite Cyclops in publications use:")
 
 bibentry(bibtype = "Article",
-        author = personList(as.person("M. A. Suchard"),
-                            as.person("S. E. Simpson"),
-                            as.person("I. Zorych"),
-                            as.person("P. Ryan"),
-                            as.person("D. Madigan")),
+        author = c(as.person("M. A. Suchard"),
+                   as.person("S. E. Simpson"),
+                   as.person("I. Zorych"),
+                   as.person("P. Ryan"),
+                   as.person("D. Madigan")),
         title = "Massive parallelization of serial inference algorithms for complex generalized linear models",
         journal = "ACM Transactions on Modeling and Computer Simulation",
         volume = "23",

diff --git a/man/Cyclops-package.Rd b/man/Cyclops-package.Rd
diff --git a/man/convertToCyclopsData.Rd b/man/convertToCyclopsData.Rd
diff --git a/man/survfit.cyclopsFit.Rd b/man/survfit.cyclopsFit.Rd
diff --git a/src/Makevars → src/Makevars.in b/src/Makevars → src/Makevars.in
@@ -1,6 +1,7 @@
 CUDA_HOME = /usr/local/cuda
 
 CUB_PATH = $(CUDA_HOME)/include
+#CUB_PATH = /home/jianxiao/cub_1.8.0/cub
 
 ## Use the R_HOME indirection to support installations of multiple R version
 PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` -lOpenCL -pthread -L$(CUDA_HOME)/lib64 -lcuda -lcudart

diff --git a/src/Makevars.win → src/Makevars.win.in b/src/Makevars.win → src/Makevars.win.in
@@ -24,8 +24,6 @@ PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"`
 ## done by a number of packages, but recommended only for more advanced users
 ## comfortable with autoconf and its related tools.
 
-CXX_STD = CXX11
-
 PKG_CPPFLAGS = -I. -Icyclops -DR_BUILD -DWIN_BUILD -DDOUBLE_PRECISION -DRCPP_PARALLEL_USE_TBB=1
 
 # PKG_LIBS += $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" \
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		#!/bin/sh

		rm -f config.* src/Makevars src/Markvars.win src/config.h