From acecd189fff1792b86c8240770f940961d982b70 Mon Sep 17 00:00:00 2001 From: Jeff Date: Sat, 31 Aug 2024 17:10:44 -0400 Subject: [PATCH] fixing remap for a couple cpp files --- src/intPGOcc.cpp | 1 + src/svcTPGOccNNGP.cpp | 121 +++++++++++++++++------------------ src/svcTPGOccNNGPPredict.cpp | 25 ++++---- 3 files changed, 74 insertions(+), 73 deletions(-) diff --git a/src/intPGOcc.cpp b/src/intPGOcc.cpp index a62795e..16369a4 100755 --- a/src/intPGOcc.cpp +++ b/src/intPGOcc.cpp @@ -7,6 +7,7 @@ #include #endif +#define R_NO_REMAP #include #include #include diff --git a/src/svcTPGOccNNGP.cpp b/src/svcTPGOccNNGP.cpp index f7b3021..3a519e7 100755 --- a/src/svcTPGOccNNGP.cpp +++ b/src/svcTPGOccNNGP.cpp @@ -7,6 +7,7 @@ #include #endif +#define R_NO_REMAP #include #include #include @@ -48,8 +49,8 @@ void updateBFSVCT(double *B, double *F, double *c, double *C, double *coords, in C[mm*threadID+l*nnIndxLU[n+i]+k] = sigmaSq*spCor(e, phi, nu, covModel, &bk[threadID*nb]); } } - F77_NAME(dpotrf)(&lower, &nnIndxLU[n+i], &C[mm*threadID], &nnIndxLU[n+i], &info FCONE); if(info != 0){error("c++ error: dpotrf failed\n");} - F77_NAME(dpotri)(&lower, &nnIndxLU[n+i], &C[mm*threadID], &nnIndxLU[n+i], &info FCONE); if(info != 0){error("c++ error: dpotri failed\n");} + F77_NAME(dpotrf)(&lower, &nnIndxLU[n+i], &C[mm*threadID], &nnIndxLU[n+i], &info FCONE); if(info != 0){Rf_error("c++ error: dpotrf failed\n");} + F77_NAME(dpotri)(&lower, &nnIndxLU[n+i], &C[mm*threadID], &nnIndxLU[n+i], &info FCONE); if(info != 0){Rf_error("c++ error: dpotri failed\n");} F77_NAME(dsymv)(&lower, &nnIndxLU[n+i], &one, &C[mm*threadID], &nnIndxLU[n+i], &c[m*threadID], &inc, &zero, &B[nnIndxLU[i]], &inc FCONE); F[i] = sigmaSq - F77_NAME(ddot)(&nnIndxLU[n+i], &B[nnIndxLU[i]], &inc, &c[m*threadID], &inc); }else{ @@ -196,7 +197,7 @@ extern "C" { omp_set_num_threads(nThreads); #else if(nThreads > 1){ - warning("n.omp.threads > %i, but source not compiled with OpenMP support.", nThreads); + Rf_warning("n.omp.threads > %i, but source not compiled with OpenMP support.", nThreads); nThreads = 1; } #endif @@ -285,46 +286,46 @@ extern "C" { * Return Stuff * *******************************************************************/ SEXP betaSamples_r; - PROTECT(betaSamples_r = allocMatrix(REALSXP, pOcc, nPost)); nProtect++; + PROTECT(betaSamples_r = Rf_allocMatrix(REALSXP, pOcc, nPost)); nProtect++; zeros(REAL(betaSamples_r), pOcc * nPost); SEXP alphaSamples_r; - PROTECT(alphaSamples_r = allocMatrix(REALSXP, pDet, nPost)); nProtect++; + PROTECT(alphaSamples_r = Rf_allocMatrix(REALSXP, pDet, nPost)); nProtect++; zeros(REAL(alphaSamples_r), pDet * nPost); SEXP zSamples_r; - PROTECT(zSamples_r = allocMatrix(REALSXP, JnYears, nPost)); nProtect++; + PROTECT(zSamples_r = Rf_allocMatrix(REALSXP, JnYears, nPost)); nProtect++; zeros(REAL(zSamples_r), JnYears * nPost); SEXP wSamples_r; - PROTECT(wSamples_r = allocMatrix(REALSXP, JwpTilde, nPost)); nProtect++; + PROTECT(wSamples_r = Rf_allocMatrix(REALSXP, JwpTilde, nPost)); nProtect++; zeros(REAL(wSamples_r), JwpTilde * nPost); SEXP etaSamples_r; if (ar1) { - PROTECT(etaSamples_r = allocMatrix(REALSXP, nYearsMax, nPost)); nProtect++; + PROTECT(etaSamples_r = Rf_allocMatrix(REALSXP, nYearsMax, nPost)); nProtect++; zeros(REAL(etaSamples_r), nYearsMax * nPost); } SEXP psiSamples_r; - PROTECT(psiSamples_r = allocMatrix(REALSXP, JnYears, nPost)); nProtect++; + PROTECT(psiSamples_r = Rf_allocMatrix(REALSXP, JnYears, nPost)); nProtect++; zeros(REAL(psiSamples_r), JnYears * nPost); // Detection random effects SEXP sigmaSqPSamples_r; SEXP alphaStarSamples_r; if (pDetRE > 0) { - PROTECT(sigmaSqPSamples_r = allocMatrix(REALSXP, pDetRE, nPost)); nProtect++; + PROTECT(sigmaSqPSamples_r = Rf_allocMatrix(REALSXP, pDetRE, nPost)); nProtect++; zeros(REAL(sigmaSqPSamples_r), pDetRE * nPost); - PROTECT(alphaStarSamples_r = allocMatrix(REALSXP, nDetRE, nPost)); nProtect++; + PROTECT(alphaStarSamples_r = Rf_allocMatrix(REALSXP, nDetRE, nPost)); nProtect++; zeros(REAL(alphaStarSamples_r), nDetRE * nPost); } // Occurrence random effects SEXP sigmaSqPsiSamples_r; SEXP betaStarSamples_r; if (pOccRE > 0) { - PROTECT(sigmaSqPsiSamples_r = allocMatrix(REALSXP, pOccRE, nPost)); nProtect++; + PROTECT(sigmaSqPsiSamples_r = Rf_allocMatrix(REALSXP, pOccRE, nPost)); nProtect++; zeros(REAL(sigmaSqPsiSamples_r), pOccRE * nPost); - PROTECT(betaStarSamples_r = allocMatrix(REALSXP, nOccRE, nPost)); nProtect++; + PROTECT(betaStarSamples_r = Rf_allocMatrix(REALSXP, nOccRE, nPost)); nProtect++; zeros(REAL(betaStarSamples_r), nOccRE * nPost); } // Likelihood samples for WAIC. SEXP likeSamples_r; - PROTECT(likeSamples_r = allocMatrix(REALSXP, JnYears, nPost)); nProtect++; + PROTECT(likeSamples_r = Rf_allocMatrix(REALSXP, JnYears, nPost)); nProtect++; zeros(REAL(likeSamples_r), J * nPost); /********************************************************************** @@ -378,17 +379,17 @@ extern "C" { // For normal priors // Occupancy regression coefficient priors. F77_NAME(dpotrf)(lower, &pOcc, SigmaBetaInv, &pOcc, &info FCONE); - if(info != 0){error("c++ error: dpotrf SigmaBetaInv failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf SigmaBetaInv failed\n");} F77_NAME(dpotri)(lower, &pOcc, SigmaBetaInv, &pOcc, &info FCONE); - if(info != 0){error("c++ error: dpotri SigmaBetaInv failed\n");} + if(info != 0){Rf_error("c++ error: dpotri SigmaBetaInv failed\n");} double *SigmaBetaInvMuBeta = (double *) R_alloc(pOcc, sizeof(double)); F77_NAME(dsymv)(lower, &pOcc, &one, SigmaBetaInv, &pOcc, muBeta, &inc, &zero, SigmaBetaInvMuBeta, &inc FCONE); // Detection regression coefficient priors. F77_NAME(dpotrf)(lower, &pDet, SigmaAlphaInv, &pDet, &info FCONE); - if(info != 0){error("c++ error: dpotrf SigmaAlphaInv failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf SigmaAlphaInv failed\n");} F77_NAME(dpotri)(lower, &pDet, SigmaAlphaInv, &pDet, &info FCONE); - if(info != 0){error("c++ error: dpotri SigmaAlphaInv failed\n");} + if(info != 0){Rf_error("c++ error: dpotri SigmaAlphaInv failed\n");} double *SigmaAlphaInvMuAlpha = (double *) R_alloc(pDet, sizeof(double)); F77_NAME(dsymv)(lower, &pDet, &one, SigmaAlphaInv, &pDet, muAlpha, &inc, &zero, SigmaAlphaInvMuAlpha, &inc FCONE); @@ -456,13 +457,13 @@ extern "C" { double logDet; double phiCand = 0.0, nuCand = 0.0, rhoCand = 0.0, sigmaSqCand = 0.0; SEXP acceptSamples_r; - PROTECT(acceptSamples_r = allocMatrix(REALSXP, nThetaSave, nBatch)); nProtect++; + PROTECT(acceptSamples_r = Rf_allocMatrix(REALSXP, nThetaSave, nBatch)); nProtect++; zeros(REAL(acceptSamples_r), nThetaSave * nBatch); SEXP tuningSamples_r; - PROTECT(tuningSamples_r = allocMatrix(REALSXP, nThetaSave, nBatch)); nProtect++; + PROTECT(tuningSamples_r = Rf_allocMatrix(REALSXP, nThetaSave, nBatch)); nProtect++; zeros(REAL(tuningSamples_r), nThetaSave * nBatch); SEXP thetaSamples_r; - PROTECT(thetaSamples_r = allocMatrix(REALSXP, nThetaSave, nPost)); nProtect++; + PROTECT(thetaSamples_r = Rf_allocMatrix(REALSXP, nThetaSave, nPost)); nProtect++; zeros(REAL(thetaSamples_r), nThetaSave * nPost); double b, e, aij, aa; double *a = (double *) R_alloc(pTilde, sizeof(double)); @@ -527,9 +528,9 @@ extern "C" { AR1(nYearsMax, theta[rhoIndx], theta[sigmaSqTIndx], SigmaEta); clearUT(SigmaEta, nYearsMax); F77_NAME(dpotrf)(lower, &nYearsMax, SigmaEta, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: Cholesky failed in initial time covariance matrix\n");} + if(info != 0){Rf_error("c++ error: Cholesky failed in initial time covariance matrix\n");} F77_NAME(dpotri)(lower, &nYearsMax, SigmaEta, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: Cholesky inverse failed in initial time covariance matrix\n");} + if(info != 0){Rf_error("c++ error: Cholesky inverse failed in initial time covariance matrix\n");} } double *eta = (double *) R_alloc(nYearsMax, sizeof(double)); zeros(eta, nYearsMax); // For sigmaSqT sampler @@ -630,12 +631,12 @@ extern "C" { F77_NAME(dpotrf)(lower, &pOcc, tmp_ppOcc, &pOcc, &info FCONE); - if(info != 0){error("c++ error: dpotrf A.beta failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf A.beta failed\n");} F77_NAME(dpotri)(lower, &pOcc, tmp_ppOcc, &pOcc, &info FCONE); - if(info != 0){error("c++ error: dpotri A.beta failed\n");} + if(info != 0){Rf_error("c++ error: dpotri A.beta failed\n");} F77_NAME(dsymv)(lower, &pOcc, &one, tmp_ppOcc, &pOcc, tmp_pOcc, &inc, &zero, tmp_pOcc2, &inc FCONE); F77_NAME(dpotrf)(lower, &pOcc, tmp_ppOcc, &pOcc, &info FCONE); - if(info != 0){error("c++ error: dpotrf A.beta2 failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf A.beta2 failed\n");} mvrnorm(beta, tmp_pOcc2, tmp_ppOcc, pOcc); /******************************************************************** @@ -677,12 +678,12 @@ extern "C" { } // j F77_NAME(dpotrf)(lower, &pDet, tmp_ppDet, &pDet, &info FCONE); - if(info != 0){error("c++ error: dpotrf A.alpha failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf A.alpha failed\n");} F77_NAME(dpotri)(lower, &pDet, tmp_ppDet, &pDet, &info FCONE); - if(info != 0){error("c++ error: dpotri A.alpha failed\n");} + if(info != 0){Rf_error("c++ error: dpotri A.alpha failed\n");} F77_NAME(dsymv)(lower, &pDet, &one, tmp_ppDet, &pDet, tmp_pDet, &inc, &zero, tmp_pDet2, &inc FCONE); F77_NAME(dpotrf)(lower, &pDet, tmp_ppDet, &pDet, &info FCONE); - if(info != 0){error("c++ error: dpotrf here failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf here failed\n");} mvrnorm(alpha, tmp_pDet2, tmp_ppDet, pDet); /******************************************************************** @@ -842,9 +843,9 @@ extern "C" { var[k * pTilde + k] += ff[k] + v[k]; } // k F77_NAME(dpotrf)(lower, &pTilde, var, &pTilde, &info FCONE); - if(info != 0){error("c++ error: dpotrf var failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf var failed\n");} F77_NAME(dpotri)(lower, &pTilde, var, &pTilde, &info FCONE); - if(info != 0){error("c++ error: dpotri var failed\n");} + if(info != 0){Rf_error("c++ error: dpotri var failed\n");} // mu zeros(mu, pTilde); @@ -865,7 +866,7 @@ extern "C" { F77_NAME(dsymv)(lower, &pTilde, &one, var, &pTilde, mu, &inc, &zero, tmp_pTilde, &inc FCONE); F77_NAME(dpotrf)(lower, &pTilde, var, &pTilde, &info FCONE); - if(info != 0){error("c++ error: dpotrf var 2 failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf var 2 failed\n");} mvrnorm(&w[ii * pTilde], tmp_pTilde, var, pTilde); } // ii (site) @@ -1019,9 +1020,9 @@ extern "C" { AR1(nYearsMax, theta[rhoIndx], 1.0, SigmaEta); clearUT(SigmaEta, nYearsMax); F77_NAME(dpotrf)(lower, &nYearsMax, SigmaEta, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: Cholesky failed in covariance matrix\n");} + if(info != 0){Rf_error("c++ error: Cholesky failed in covariance matrix\n");} F77_NAME(dpotri)(lower, &nYearsMax, SigmaEta, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: Cholesky inverse failed in covariance matrix\n");} + if(info != 0){Rf_error("c++ error: Cholesky inverse failed in covariance matrix\n");} fillUTri(SigmaEta, nYearsMax); // Compute t(eta) %*% SigmaEta^-1 %*% eta for (t = 0; t < nYearsMax; t++) { @@ -1050,13 +1051,13 @@ extern "C" { // Invert SigmaEtaCand and log det cov. logPostCand = 0.0; F77_NAME(dpotrf)(lower, &nYearsMax, SigmaEtaCand, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: Cholesky failed in proposal covariance matrix\n");} + if(info != 0){Rf_error("c++ error: Cholesky failed in proposal covariance matrix\n");} // Get log of the determinant of the covariance matrix. for (k = 0; k < nYearsMax; k++) { logPostCand += 2.0 * log(SigmaEtaCand[k*nYearsMax+k]); } // k F77_NAME(dpotri)(lower, &nYearsMax, SigmaEtaCand, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: Cholesky inverse failed in proposal covariance matrix\n");} + if(info != 0){Rf_error("c++ error: Cholesky inverse failed in proposal covariance matrix\n");} logPostCand = 0.0; // Jacobian and Uniform prior. logPostCand += log(rhoCand - rhoA) + log(rhoB - rhoCand); @@ -1070,12 +1071,12 @@ extern "C" { clearUT(SigmaEta, nYearsMax); logPostCurr = 0.0; F77_NAME(dpotrf)(lower, &nYearsMax, SigmaEta, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: Cholesky failed in covariance matrix\n");} + if(info != 0){Rf_error("c++ error: Cholesky failed in covariance matrix\n");} for (k = 0; k < nYearsMax; k++) { logPostCurr += 2.0 * log(SigmaEta[k*nYearsMax+k]); } // k F77_NAME(dpotri)(lower, &nYearsMax, SigmaEta, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: Cholesky inverse failed in covariance matrix\n");} + if(info != 0){Rf_error("c++ error: Cholesky inverse failed in covariance matrix\n");} logPostCurr = 0.0; logPostCurr += log(rho - rhoA) + log(rhoB - rho); // (-1/2) * tmp_JD` * C^-1 * tmp_JD @@ -1118,15 +1119,15 @@ extern "C" { // Cholesky of A.eta F77_NAME(dpotrf)(lower, &nYearsMax, tmp_nnYears, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: dpotrf on A.eta failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf on A.eta failed\n");} // Inverse of A.eta F77_NAME(dpotri)(lower, &nYearsMax, tmp_nnYears, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: dpotri on A.eta failed\n");} + if(info != 0){Rf_error("c++ error: dpotri on A.eta failed\n");} // A.eta.inv %*% b.eta. Stored in tmp_ F77_NAME(dsymv)(lower, &nYearsMax, &one, tmp_nnYears, &nYearsMax, tmp_nYearsMax, &inc, &zero, tmp_nYearsMax2, &inc FCONE); F77_NAME(dpotrf)(lower, &nYearsMax, tmp_nnYears, &nYearsMax, &info FCONE); - if(info != 0){error("c++ error: dpotrf on A.eta failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf on A.eta failed\n");} // Args: destination, mu, cholesky of the covariance matrix, dimension mvrnorm(eta, tmp_nYearsMax2, tmp_nnYears, nYearsMax); } @@ -1291,8 +1292,8 @@ extern "C" { nResultListObjs += 1; } - PROTECT(result_r = allocVector(VECSXP, nResultListObjs)); nProtect++; - PROTECT(resultName_r = allocVector(VECSXP, nResultListObjs)); nProtect++; + PROTECT(result_r = Rf_allocVector(VECSXP, nResultListObjs)); nProtect++; + PROTECT(resultName_r = Rf_allocVector(VECSXP, nResultListObjs)); nProtect++; // Setting the components of the output list. SET_VECTOR_ELT(result_r, 0, betaSamples_r); @@ -1328,30 +1329,30 @@ extern "C" { } SET_VECTOR_ELT(result_r, ar1Ind, etaSamples_r); } - // mkChar turns a C string into a CHARSXP - SET_VECTOR_ELT(resultName_r, 0, mkChar("beta.samples")); - SET_VECTOR_ELT(resultName_r, 1, mkChar("alpha.samples")); - SET_VECTOR_ELT(resultName_r, 2, mkChar("z.samples")); - SET_VECTOR_ELT(resultName_r, 3, mkChar("psi.samples")); - SET_VECTOR_ELT(resultName_r, 4, mkChar("theta.samples")); - SET_VECTOR_ELT(resultName_r, 5, mkChar("w.samples")); - SET_VECTOR_ELT(resultName_r, 6, mkChar("tune")); - SET_VECTOR_ELT(resultName_r, 7, mkChar("accept")); - SET_VECTOR_ELT(resultName_r, 8, mkChar("like.samples")); + // Rf_mkChar turns a C string into a CHARSXP + SET_VECTOR_ELT(resultName_r, 0, Rf_mkChar("beta.samples")); + SET_VECTOR_ELT(resultName_r, 1, Rf_mkChar("alpha.samples")); + SET_VECTOR_ELT(resultName_r, 2, Rf_mkChar("z.samples")); + SET_VECTOR_ELT(resultName_r, 3, Rf_mkChar("psi.samples")); + SET_VECTOR_ELT(resultName_r, 4, Rf_mkChar("theta.samples")); + SET_VECTOR_ELT(resultName_r, 5, Rf_mkChar("w.samples")); + SET_VECTOR_ELT(resultName_r, 6, Rf_mkChar("tune")); + SET_VECTOR_ELT(resultName_r, 7, Rf_mkChar("accept")); + SET_VECTOR_ELT(resultName_r, 8, Rf_mkChar("like.samples")); if (pDetRE > 0) { - SET_VECTOR_ELT(resultName_r, 9, mkChar("sigma.sq.p.samples")); - SET_VECTOR_ELT(resultName_r, 10, mkChar("alpha.star.samples")); + SET_VECTOR_ELT(resultName_r, 9, Rf_mkChar("sigma.sq.p.samples")); + SET_VECTOR_ELT(resultName_r, 10, Rf_mkChar("alpha.star.samples")); } if (pOccRE > 0) { - SET_VECTOR_ELT(resultName_r, tmp_0, mkChar("sigma.sq.psi.samples")); - SET_VECTOR_ELT(resultName_r, tmp_0 + 1, mkChar("beta.star.samples")); + SET_VECTOR_ELT(resultName_r, tmp_0, Rf_mkChar("sigma.sq.psi.samples")); + SET_VECTOR_ELT(resultName_r, tmp_0 + 1, Rf_mkChar("beta.star.samples")); } if (ar1) { - SET_VECTOR_ELT(resultName_r, ar1Ind, mkChar("eta.samples")); + SET_VECTOR_ELT(resultName_r, ar1Ind, Rf_mkChar("eta.samples")); } // Set the names of the output list. - namesgets(result_r, resultName_r); + Rf_namesgets(result_r, resultName_r); //unprotect UNPROTECT(nProtect); @@ -1359,5 +1360,3 @@ extern "C" { return(result_r); } } - - diff --git a/src/svcTPGOccNNGPPredict.cpp b/src/svcTPGOccNNGPPredict.cpp index bcdb58b..7e3cb7d 100644 --- a/src/svcTPGOccNNGPPredict.cpp +++ b/src/svcTPGOccNNGPPredict.cpp @@ -6,6 +6,7 @@ #include #endif +#define R_NO_REMAP #include #include #include @@ -75,7 +76,7 @@ extern "C" { omp_set_num_threads(nThreads); #else if(nThreads > 1){ - warning("n.omp.threads > %i, but source not compiled with OpenMP support.", nThreads); + Rf_warning("n.omp.threads > %i, but source not compiled with OpenMP support.", nThreads); nThreads = 1; } #endif @@ -145,9 +146,9 @@ extern "C" { int threadID = 0, status = 0; SEXP z0_r, w0_r, psi0_r; - PROTECT(z0_r = allocMatrix(REALSXP, qnYears, nSamples)); nProtect++; - PROTECT(psi0_r = allocMatrix(REALSXP, qnYears, nSamples)); nProtect++; - PROTECT(w0_r = allocMatrix(REALSXP, Jw0pTilde, nSamples)); nProtect++; + PROTECT(z0_r = Rf_allocMatrix(REALSXP, qnYears, nSamples)); nProtect++; + PROTECT(psi0_r = Rf_allocMatrix(REALSXP, qnYears, nSamples)); nProtect++; + PROTECT(w0_r = Rf_allocMatrix(REALSXP, Jw0pTilde, nSamples)); nProtect++; double *z0 = REAL(z0_r); double *psi0 = REAL(psi0_r); double *w0 = REAL(w0_r); @@ -201,9 +202,9 @@ extern "C" { } F77_NAME(dpotrf)(lower, &m, &C[threadID*mm], &m, &info FCONE); - if(info != 0){error("c++ error: dpotrf failed\n");} + if(info != 0){Rf_error("c++ error: dpotrf failed\n");} F77_NAME(dpotri)(lower, &m, &C[threadID*mm], &m, &info FCONE); - if(info != 0){error("c++ error: dpotri failed\n");} + if(info != 0){Rf_error("c++ error: dpotri failed\n");} F77_NAME(dsymv)(lower, &m, &one, &C[threadID*mm], &m, &c[threadID*m], &inc, &zero, &tmp_m[threadID*m], &inc FCONE); @@ -265,19 +266,19 @@ extern "C" { SEXP result_r, resultName_r; int nResultListObjs = 3; - PROTECT(result_r = allocVector(VECSXP, nResultListObjs)); nProtect++; - PROTECT(resultName_r = allocVector(VECSXP, nResultListObjs)); nProtect++; + PROTECT(result_r = Rf_allocVector(VECSXP, nResultListObjs)); nProtect++; + PROTECT(resultName_r = Rf_allocVector(VECSXP, nResultListObjs)); nProtect++; SET_VECTOR_ELT(result_r, 0, z0_r); - SET_VECTOR_ELT(resultName_r, 0, mkChar("z.0.samples")); + SET_VECTOR_ELT(resultName_r, 0, Rf_mkChar("z.0.samples")); SET_VECTOR_ELT(result_r, 1, w0_r); - SET_VECTOR_ELT(resultName_r, 1, mkChar("w.0.samples")); + SET_VECTOR_ELT(resultName_r, 1, Rf_mkChar("w.0.samples")); SET_VECTOR_ELT(result_r, 2, psi0_r); - SET_VECTOR_ELT(resultName_r, 2, mkChar("psi.0.samples")); + SET_VECTOR_ELT(resultName_r, 2, Rf_mkChar("psi.0.samples")); - namesgets(result_r, resultName_r); + Rf_namesgets(result_r, resultName_r); //unprotect UNPROTECT(nProtect);