v3.3.1

.Rbuildignore

@@ -36,3 +36,5 @@ deprecated
 .covrignore
 src/Makevars$
 src/Makevars.win$
+to_fix*
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 3.3.1
+Date: 2023-04-09 20:06:33 UTC
+SHA: d88c531efa06933c1007cb785343f1382c95ee0d

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Cyclops
 Type: Package
 Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
-Version: 3.3.0
+Version: 3.3.1
 Authors@R: c(
     person("Marc A.", "Suchard", email = "msuchard@ucla.edu", role = c("aut","cre")),
     person("Martijn J.", "Schuemie", role = "aut"),
@@ -51,4 +51,4 @@ Suggests:
     ggplot2,
     microbenchmark,
     cmprsk
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3

NEWS.md

@@ -1,3 +1,12 @@
+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
 ==============
 

cran-comments.md

@@ -1,16 +1,23 @@
-## Initial submission of patch update to package
+## Resubmission after VALGRIND feedback from Brian Ripley
 
-* fixed all WARNINGS, including generic-inconsistency, uninitialized values
-* fixed NOTE about C++11
+* 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 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 or WARNINGs
-* There is 1 occasional NOTE:
+* There is 1 occasional NOTE (besides days since last submission):
     checking installed package size ... NOTE
     installed size is 22.5Mb
     sub-directories of 1Mb or more:
@@ -23,4 +30,6 @@ 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.

src/RcppCyclopsInterface.cpp

@@ -622,8 +622,8 @@ void RcppCcdInterface::appendRList(Rcpp::List& list, const Rcpp::List& append) {
 }
 
 void RcppCcdInterface::handleError(const std::string& str) {
-//	Rcpp::stop(str); // TODO Want this to work
-	::Rf_error(str.c_str());
+    Rcpp::stop(str);
+	// ::Rf_error(str.c_str());
 }
 
 bsccs::ConvergenceType RcppCcdInterface::parseConvergenceType(const std::string& convergenceName) {
@@ -946,7 +946,7 @@ void RcppCcdInterface::initializeModelImpl(
 //  	}
 //  	singlePrior->setVariance(0, arguments.hyperprior);
 
- 	JointPriorPtr prior;
+ 	JointPriorPtr prior = nullptr;
 //  	if (arguments.flatPrior.size() == 0) {
 //  		prior = bsccs::make_shared<FullyExchangeableJointPrior>(singlePrior);
 //  	} else {

src/RcppModelData.cpp

@@ -675,7 +675,7 @@ List cyclopsReadFileData(const std::string& fileName, const std::string& modelTy
 
     //const std::vector<double>& y = ptr->getYVectorRef();
     double total = 0.0; //std::accumulate(y.begin(), y.end(), 0.0);
-    // delete reader; // TODO Test
+    delete reader; // TODO Use smart_ptr
 
     double time = timer();
     List list = List::create(

src/cyclops/CyclicCoordinateDescent.cpp

@@ -54,6 +54,8 @@ CyclicCoordinateDescent::CyclicCoordinateDescent(
 	noiseLevel = NOISY;
 	initialBound = 2.0;
 
+	priorType = priors::NONE;
+
 	init(hXI.getHasOffsetCovariate());
 }
 
@@ -89,6 +91,8 @@ CyclicCoordinateDescent::CyclicCoordinateDescent(const CyclicCoordinateDescent&
 	noiseLevel = copy.noiseLevel;
 	initialBound = copy.initialBound;
 
+	priorType = copy.priorType;
+
 	init(hXI.getHasOffsetCovariate());
 
 	if (copy.hWeights.size() > 0) {

src/cyclops/engine/ModelSpecifics.hpp

@@ -1124,7 +1124,7 @@ void ModelSpecifics<BaseModel,RealType>::computeGradientAndHessianImpl(int index
 // 	    gradient = result.real();
 // 	    hessian = result.imag();
 
-        using RealTypePair = std::pair<RealType, RealType>;
+        // using RealTypePair = std::pair<RealType, RealType>;
 
 	    IteratorType it(hX, index);
 	    const int end = it.size() - 1;
@@ -1266,7 +1266,7 @@ void ModelSpecifics<BaseModel,RealType>::computeThirdDerivativeImpl(int index, d
 #endif
 
     RealType third = static_cast<RealType>(0);
-    RealType hessian = static_cast<RealType>(0);
+    // RealType hessian = static_cast<RealType>(0);
 
     if (BaseModel::cumulativeGradientAndHessian) { // Compile-time switch
 

tools/configure.R

@@ -19,5 +19,8 @@ if (getRversion() < "4.1") {
     }
 }
 
-cat(txt, file = makevars_out, sep = "\n")
-cat(txt_win, file = makevars_win_out, sep = "\n")
+if (.Platform$OS.type == "unix") {
+	cat(txt, file = makevars_out, sep = "\n")
+} else {
+	cat(txt_win, file = makevars_win_out, sep = "\n")
+}