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Merged
paciorek merged 3 commits into from
Mar 31, 2026
+192 −259
Merged

Fix find var api calls expt1 #1617

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c21482a
Update from Rf_findVar and Rf_findVarInFrame while maintaining backwa…
perrydv Mar 24, 2026
ca1fa9c
Use R_do_slot; remove R_BracketSymbol; PROTECT in getSEXPdims; remove…
perrydv Mar 30, 2026
87a61f1
Merge branch 'devel' into fix-findVar-API-calls-expt1
perrydv Mar 30, 2026
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2 changes: 1 addition & 1 deletion packages/nimble/R/cppDefs_nimbleFunction.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1204,7 +1204,7 @@ makeCopyFromRobjectDef <- function(cppCopyTypes,
quote = TRUE
)
} else {
unprotectCount <- 2 + length(copyCalls) ## 2 from SETUP_S_xData
unprotectCount <- length(copyCalls) ## 0 extra from SETUP_S_xData (1 PROTECT, covered by the +1 below)
allRcode <- do.call('call',
c(list('{'),
list(cppLiteral("SETUP_S_xData;")),
Expand Down
30 changes: 8 additions & 22 deletions packages/nimble/R/cppDefs_nimbleList.R
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Original file line number Diff line number Diff line change
Expand Up @@ -228,31 +228,24 @@ cppNimbleListClass <- setRefClass('cppNimbleListClass',

conditionalClauseStart <- list(quote(cppLiteral('if (!RCopiedFlag){')))
conditionalClauseEnd <- list(quote(cppLiteral('}')))
environmentCPPName <- Rname2CppName('S_.xData') ## create SEXP for ref class environment
listElementTable$addSymbol(cppSEXP(name = environmentCPPName))
envLine <- substitute({PROTECT(ENVNAME <- Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(ENVNAME, 0, PROTECT(Rf_mkChar(".xData")));},
list(ENVNAME = as.name(environmentCPPName)))

for(i in seq_along(elementNames)){
Snames[i] <- Rname2CppName(paste0('S_', elementNames[i]))
listElementTable$addSymbol(cppSEXP(name = Snames[i]))
elementSymTab <- nimCompProc$symTab$getSymbolObject(elementNames[i])
conditionalLineList <- c(conditionalLineList, generateConditionalLines(nimCompProc$symTab$getSymbolObject(elementNames[i]),
listElementTable$getSymbolObject(Snames[i])))

copyToListLines[[i]] <- substitute(Rf_defineVar(Rf_install(ELEMENTNAME), VALUE, PROTECT(GET_SLOT(ROBJ, XDATA))),
copyToListLines[[i]] <- substitute(Rf_defineVar(Rf_install(ELEMENTNAME), VALUE, PROTECT(R_do_slot(ROBJ, Rf_install(".xData")))),
list(ELEMENTNAME = elementNames[i], VALUE = as.name(Snames[i]),
ROBJ = as.name('RObjectPointer'),
XDATA = as.name(environmentCPPName)))
ROBJ = as.name('RObjectPointer')))
}

setFlagLine <- list(substitute(RCopiedFlag <- true,
list()))
returnLine <- list(substitute(return(ROBJ),
list(ROBJ = as.name('RObjectPointer'))))
unprotectLine <- list(substitute(UNPROTECT(N), list(N = 2 * numElements + 1 + 1)))
allCode <- embedListInRbracket(c(conditionalClauseStart, list(envLine), conditionalLineList,
unprotectLine <- list(substitute(UNPROTECT(N), list(N = 2 * numElements)))
allCode <- embedListInRbracket(c(conditionalClauseStart, conditionalLineList,
copyToListLines, setFlagLine, unprotectLine,
conditionalClauseEnd, returnLine))
functionDefs[[paste0(name, "_copyTo")]] <<- cppFunctionDef(name = "copyToSEXP",
Expand All @@ -276,26 +269,19 @@ cppNimbleListClass <- setRefClass('cppNimbleListClass',
listElementTable <- symbolTable()
storeSexpLine <- list(quote(cppLiteral('R_PreserveObject(RObjectPointer = S_nimList_);')))

environmentCPPName <- Rname2CppName('S_.xData') ## create SEXP for ref class environment
listElementTable$addSymbol(cppSEXP(name = environmentCPPName))
envLine <- substitute({PROTECT(ENVNAME <- Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(ENVNAME, 0, PROTECT(Rf_mkChar(".xData")));},
list(ENVNAME = as.name(environmentCPPName)))

for(i in seq_along(argNames)) {
Snames[i] <- Rname2CppName(paste0('S_', argNames[i]))
listElementTable$addSymbol(cppSEXP(name = Snames[i]))
copyFromListLines[[i]] <- substitute(PROTECT(SVAR <- NIM_FINDVARINFRAME(PROTECT(GET_SLOT(S_nimList_, XDATA)), Rf_install(ARGNAME))),
copyFromListLines[[i]] <- substitute(PROTECT(SVAR <- NIM_FINDVARINFRAME(PROTECT(R_do_slot(S_nimList_, Rf_install(".xData"))), Rf_install(ARGNAME))),
list(ARGNAME = argNames[i],
SVAR = as.name(Snames[i]),
XDATA = as.name(environmentCPPName)))
SVAR = as.name(Snames[i])))
copyLine <- buildCopyLineFromSEXP(listElementTable$getSymbolObject(Snames[i]),
nimCompProc$symTab$getSymbolObject(argNames[i]))
copyLines <- c(copyLines, copyLine)
}
numArgs <- length(argNames)
unprotectLine <- substitute(UNPROTECT(N), list(N = 2 * numArgs + 1 + 1))
allCode <- embedListInRbracket(c(storeSexpLine, envLine,
unprotectLine <- substitute(UNPROTECT(N), list(N = 2 * numArgs))
allCode <- embedListInRbracket(c(storeSexpLine,
copyFromListLines, copyLines,
list(unprotectLine)))
functionDefs[[paste0(name, "_copyFrom")]] <<- cppFunctionDef(name = "copyFromSEXP",
Expand Down
17 changes: 7 additions & 10 deletions packages/nimble/inst/CppCode/RcppNimbleUtils.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -54,16 +54,13 @@ SEXP setDoublePtrFromSinglePtr(SEXP SdoublePtr, SEXP SsinglePtr) {
void setNimbleFxnPtr_copyFromRobject(void *nf_to, SEXP S_NF_from) {
void **doublePtr = static_cast<void **>(nf_to);
SEXP Scnf, SsinglePtr;
SEXP S_pxData;
PROTECT(S_pxData = Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(S_pxData, 0, Rf_mkChar(".xData"));
// environment(modelVar)$.CobjectInterface
PROTECT(Scnf = NIM_FINDVARINFRAME(PROTECT(GET_SLOT(
PROTECT(Scnf = NIM_FINDVARINFRAME(PROTECT(R_do_slot(
S_NF_from,
S_pxData)),
Rf_install(".xData"))),
Rf_install(".CobjectInterface"))
);
int unprotectCount = 3;
int unprotectCount = 2;
if(Rf_isNewList(Scnf)) {
// multi-interface
//Cnf[[1]]$basePtrList[[ Cnf[[2]] ]]
Expand All @@ -72,10 +69,10 @@ void setNimbleFxnPtr_copyFromRobject(void *nf_to, SEXP S_NF_from) {
int index = (Rf_isInteger(Sindex) ? INTEGER(Sindex)[0] : REAL(Sindex)[0]);
index--; // From 1-based to 0-based indexing
PROTECT(SsinglePtr = VECTOR_ELT(
NIM_FINDVARINFRAME(PROTECT(GET_SLOT(
NIM_FINDVARINFRAME(PROTECT(R_do_slot(
VECTOR_ELT(Scnf,
0),
S_pxData)),
Rf_install(".xData"))),
Rf_install("basePtrList")),
index
)
Expand All @@ -85,9 +82,9 @@ void setNimbleFxnPtr_copyFromRobject(void *nf_to, SEXP S_NF_from) {
// printf("in non-list\n");
// full interface
// Cnf$.basePtr
PROTECT(SsinglePtr = NIM_FINDVARINFRAME(PROTECT(GET_SLOT(
PROTECT(SsinglePtr = NIM_FINDVARINFRAME(PROTECT(R_do_slot(
Scnf,
S_pxData)),
Rf_install(".xData"))),
Rf_install(".basePtr")));
unprotectCount += 2;
}
Expand Down
7 changes: 5 additions & 2 deletions packages/nimble/inst/CppCode/RcppUtils.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,10 @@ vector<int> getSEXPdims(SEXP Sx) {
vector<int> ans;
ans.resize(1); ans[0] = LENGTH(Sx); return(ans);
}
return(SEXP_2_vectorInt(Rf_getAttrib(Sx, R_DimSymbol), 0));
SEXP dims = PROTECT(Rf_getAttrib(Sx, R_DimSymbol));
vector<int> result = SEXP_2_vectorInt(dims, 0);
UNPROTECT(1);
return result;
}

string STRSEXP_2_string(SEXP Ss, int i) {
Expand Down Expand Up @@ -858,7 +861,7 @@ SEXP varAndIndices_2_LANGSXP(const varAndIndicesClass &varAndInds) {
Sans = PROTECT(Rf_install(varAndInds.varName.c_str()));
} else {
t = Sans = PROTECT(Rf_allocVector(LANGSXP, ansLen));
SETCAR(t, R_BracketSymbol); t = CDR(t);
SETCAR(t, Rf_install("[")); t = CDR(t);
SETCAR(t, Rf_install(varAndInds.varName.c_str())); t = CDR(t);
for(size_t i = 0; i < varAndInds.indices.size(); ++i) {
if(varAndInds.indices[i].size() == 0) { // blank
Expand Down
34 changes: 14 additions & 20 deletions packages/nimble/inst/CppCode/accessorClasses.cpp
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Expand Up @@ -920,35 +920,32 @@ void populateNodeFxnVectorNew_internal_forDerivs(NodeVectorClassNew_derivs* nfv,

void populateNodeFxnVectorNew_copyFromRobject_forDerivs(void *nodeFxnVec_to, SEXP S_nodeFxnVec_from ) {
SEXP S_indexingInfo;
SEXP S_pxData;
PROTECT(S_pxData = Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(S_pxData, 0, Rf_mkChar(".xData"));
PROTECT(S_indexingInfo = VECTOR_ELT(S_nodeFxnVec_from, 1));
SEXP S_declIDs;
PROTECT(S_declIDs = VECTOR_ELT(S_indexingInfo, 0));
SEXP S_rowIndices;
PROTECT(S_rowIndices = VECTOR_ELT(S_indexingInfo, 1));
SEXP S_numberedPtrs;
PROTECT(S_numberedPtrs = PROTECT(NIM_FINDVARINFRAME(PROTECT(GET_SLOT(
PROTECT(NIM_FINDVARINFRAME(PROTECT(GET_SLOT(
PROTECT(NIM_FINDVARINFRAME(PROTECT(GET_SLOT(
PROTECT(S_numberedPtrs = PROTECT(NIM_FINDVARINFRAME(PROTECT(R_do_slot(
PROTECT(NIM_FINDVARINFRAME(PROTECT(R_do_slot(
PROTECT(NIM_FINDVARINFRAME(PROTECT(R_do_slot(
VECTOR_ELT(S_nodeFxnVec_from,
2
),
S_pxData)),
Rf_install(".xData"))),
Rf_install("CobjectInterface")
)),
S_pxData)),
Rf_install(".xData"))),
Rf_install(".nodeFxnPointers_byDeclID"))),
S_pxData)),
Rf_install(".xData"))),
Rf_install(".ptr")
))
);
SEXP SderivInfo;
PROTECT(SderivInfo = VECTOR_ELT(S_nodeFxnVec_from, 3));
NodeVectorClassNew_derivs* nfv_derivs = static_cast<NodeVectorClassNew_derivs*>(nodeFxnVec_to);
populateNodeFxnVectorNew_internal_forDerivs(nfv_derivs, S_declIDs, S_numberedPtrs, S_rowIndices, SderivInfo);
UNPROTECT(12);
UNPROTECT(11);
}

SEXP populateNodeFxnVectorNew_byDeclID_forDerivs(SEXP SnodeFxnVec, SEXP S_GIDs, SEXP SnumberedObj, SEXP S_ROWINDS, SEXP SderivInfo){
Expand Down Expand Up @@ -979,9 +976,6 @@ void populateNodeFxnVectorNew_internal(NodeVectorClassNew* nfv, SEXP S_GIDs, SEX

void populateNodeFxnVectorNew_copyFromRobject(void *nodeFxnVec_to, SEXP S_nodeFxnVec_from ) {
SEXP S_indexingInfo;
SEXP S_pxData;
S_pxData = PROTECT(Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(S_pxData, 0, Rf_mkChar(".xData"));
S_indexingInfo = PROTECT(VECTOR_ELT(S_nodeFxnVec_from, 1));
SEXP S_declIDs;
S_declIDs = PROTECT(VECTOR_ELT(S_indexingInfo, 0));
Expand All @@ -990,24 +984,24 @@ void populateNodeFxnVectorNew_copyFromRobject(void *nodeFxnVec_to, SEXP S_nodeFx
SEXP S_numberedPtrs;
// equivalent to S_nodeFxnVec_from[["model"]]$CobjectInterface$.nodeFxnPointers_byDeclID$.ptr
// implemented by S_nodeFxnVec_from[[2]]@.xData[["CobjectInterface"]]@.xData[[".nodeFxnPointers_byDeclID"]]@.xData[[".ptr"]]
S_numberedPtrs = PROTECT(NIM_FINDVARINFRAME(PROTECT(GET_SLOT(
PROTECT(NIM_FINDVARINFRAME(PROTECT(GET_SLOT(
PROTECT(NIM_FINDVARINFRAME(PROTECT(GET_SLOT(
S_numberedPtrs = PROTECT(NIM_FINDVARINFRAME(PROTECT(R_do_slot(
PROTECT(NIM_FINDVARINFRAME(PROTECT(R_do_slot(
PROTECT(NIM_FINDVARINFRAME(PROTECT(R_do_slot(
VECTOR_ELT(S_nodeFxnVec_from,
2
),
S_pxData)),
Rf_install(".xData"))),
Rf_install("CobjectInterface")
)),
S_pxData)),
Rf_install(".xData"))),
Rf_install(".nodeFxnPointers_byDeclID"))),
S_pxData)),
Rf_install(".xData"))),
Rf_install(".ptr")
)
);
NodeVectorClassNew* nfv = static_cast<NodeVectorClassNew*>(nodeFxnVec_to);
populateNodeFxnVectorNew_internal(nfv, S_declIDs, S_numberedPtrs, S_rowIndices);
UNPROTECT(10);
UNPROTECT(9);
}

SEXP populateNodeFxnVectorNew_byDeclID(SEXP SnodeFxnVec, SEXP S_GIDs, SEXP SnumberedObj, SEXP S_ROWINDS){
Expand Down
40 changes: 14 additions & 26 deletions packages/nimble/inst/CppCode/eigenUsingClasses.cpp
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Expand Up @@ -71,17 +71,14 @@ void SEXP_2_NimArr<1>(SEXP Sn, NimArr<1, int> &ans) {

/*EIGEN_EIGEN class functions below */
SEXP EIGEN_EIGENCLASS_R::copyToSEXP ( ) {
SEXP S_pxData;
SEXP S_values;
SEXP S_vectors;

PROTECT(S_pxData = Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(S_pxData, 0, Rf_mkChar(".xData"));
PROTECT(S_values = NimArr_2_SEXP<1>(values));
PROTECT(S_vectors = NimArr_2_SEXP<2>(vectors));
Rf_defineVar(Rf_install("values"), S_values, PROTECT(GET_SLOT(RObjectPointer, S_pxData)));
Rf_defineVar(Rf_install("vectors"), S_vectors, PROTECT(GET_SLOT(RObjectPointer, S_pxData)));
UNPROTECT(5);
Rf_defineVar(Rf_install("values"), S_values, PROTECT(R_do_slot(RObjectPointer, Rf_install(".xData"))));
Rf_defineVar(Rf_install("vectors"), S_vectors, PROTECT(R_do_slot(RObjectPointer, Rf_install(".xData"))));
UNPROTECT(4);

return(RObjectPointer);
}
Expand All @@ -97,36 +94,30 @@ void EIGEN_EIGENCLASS_R::createNewSEXP ( ) {
}

void EIGEN_EIGENCLASS_R::copyFromSEXP ( SEXP S_nimList_ ) {
SEXP S_pxData;
SEXP S_values;
SEXP S_vectors;
RObjectPointer = S_nimList_;
PROTECT(S_pxData = Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(S_pxData, 0, Rf_mkChar(".xData"));
PROTECT(S_values = NIM_FINDVARINFRAME(PROTECT(GET_SLOT(S_nimList_, S_pxData)), Rf_install("values")));
PROTECT(S_vectors = NIM_FINDVARINFRAME(PROTECT(GET_SLOT(S_nimList_, S_pxData)), Rf_install("vectors")));
PROTECT(S_values = NIM_FINDVARINFRAME(PROTECT(R_do_slot(S_nimList_, Rf_install(".xData"))), Rf_install("values")));
PROTECT(S_vectors = NIM_FINDVARINFRAME(PROTECT(R_do_slot(S_nimList_, Rf_install(".xData"))), Rf_install("vectors")));
SEXP_2_NimArr<1>(S_values, values);
SEXP_2_NimArr<2>(S_vectors, vectors);
UNPROTECT(5);
UNPROTECT(4);
}


/*EIGEN_SVD class functions below */
SEXP EIGEN_SVDCLASS_R::copyToSEXP ( ) {
SEXP S_pxData;
SEXP S_d;
SEXP S_u;
SEXP S_v;

PROTECT(S_pxData = Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(S_pxData, 0, Rf_mkChar(".xData"));
PROTECT(S_d = NimArr_2_SEXP<1>(d));
PROTECT(S_u = NimArr_2_SEXP<2>(u));
PROTECT(S_v = NimArr_2_SEXP<2>(v));
Rf_defineVar(Rf_install("d"), S_d, PROTECT(GET_SLOT(RObjectPointer, S_pxData)));
Rf_defineVar(Rf_install("u"), S_u, PROTECT(GET_SLOT(RObjectPointer, S_pxData)));
Rf_defineVar(Rf_install("v"), S_v, PROTECT(GET_SLOT(RObjectPointer, S_pxData)));
UNPROTECT(7);
Rf_defineVar(Rf_install("d"), S_d, PROTECT(R_do_slot(RObjectPointer, Rf_install(".xData"))));
Rf_defineVar(Rf_install("u"), S_u, PROTECT(R_do_slot(RObjectPointer, Rf_install(".xData"))));
Rf_defineVar(Rf_install("v"), S_v, PROTECT(R_do_slot(RObjectPointer, Rf_install(".xData"))));
UNPROTECT(6);

return(RObjectPointer);
}
Expand All @@ -142,20 +133,17 @@ void EIGEN_EIGENCLASS_R::copyFromSEXP ( SEXP S_nimList_ ) {
}

void EIGEN_SVDCLASS_R::copyFromSEXP ( SEXP S_nimList_ ) {
SEXP S_pxData;
SEXP S_d;
SEXP S_v;
SEXP S_u;
RObjectPointer = S_nimList_;
PROTECT(S_pxData = Rf_allocVector(STRSXP, 1));
SET_STRING_ELT(S_pxData, 0, Rf_mkChar(".xData"));
PROTECT(S_d = NIM_FINDVARINFRAME(PROTECT(GET_SLOT(S_nimList_, S_pxData)), Rf_install("d")));
PROTECT(S_v = NIM_FINDVARINFRAME(PROTECT(GET_SLOT(S_nimList_, S_pxData)), Rf_install("v")));
PROTECT(S_u = NIM_FINDVARINFRAME(PROTECT(GET_SLOT(S_nimList_, S_pxData)), Rf_install("u")));
PROTECT(S_d = NIM_FINDVARINFRAME(PROTECT(R_do_slot(S_nimList_, Rf_install(".xData"))), Rf_install("d")));
PROTECT(S_v = NIM_FINDVARINFRAME(PROTECT(R_do_slot(S_nimList_, Rf_install(".xData"))), Rf_install("v")));
PROTECT(S_u = NIM_FINDVARINFRAME(PROTECT(R_do_slot(S_nimList_, Rf_install(".xData"))), Rf_install("u")));
SEXP_2_NimArr<1>(S_d, d);
SEXP_2_NimArr<2>(S_v, v);
SEXP_2_NimArr<2>(S_u, u);
UNPROTECT(7);
UNPROTECT(6);
}

SEXP C_nimEigen(SEXP S_x, SEXP S_symmetric, SEXP S_valuesOnly, SEXP returnList) {
Expand Down
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