fix lack of openmp with macos

helske · Sep 6, 2024 · 6bebc7f · 6bebc7f
1 parent 07cadaa
commit 6bebc7f
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Showing 21 changed files with 23 additions and 20 deletions.
diff --git a/src/EM.cpp b/src/EM.cpp
@@ -1,7 +1,7 @@
 // EM algorithm for non-mixture hidden Markov models
 
 #include "forward_backward.h"
-#include <omp.h>
+#include "useomp.h"
 // [[Rcpp::export]]
 
 Rcpp::List EM(const arma::mat& transition_, const arma::cube& emission_, const arma::vec& init_,

diff --git a/src/EMx.cpp b/src/EMx.cpp
@@ -2,7 +2,7 @@
 #include "forward_backward.h"
 #include "optcoef.h"
 #include "reparma.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::List EMx(const arma::mat& transition_, const arma::cube& emission_, const arma::vec& init_,

diff --git a/src/forwardbackward.cpp b/src/forwardbackward.cpp
@@ -1,6 +1,6 @@
 // Forward-backward algorithm for non-mixture hidden Markov models
 #include "forward_backward.h"
-#include <omp.h>
+#include "useomp.h"
 // [[Rcpp::export]]
 Rcpp::List forwardbackward(const arma::mat& transition, const arma::cube& emission,
   const arma::vec& init, const arma::ucube& obs, bool forwardonly, unsigned int threads) {

diff --git a/src/forwardbackwardx.cpp b/src/forwardbackwardx.cpp
@@ -1,7 +1,7 @@
 // Forward-backward algorithm for mixture hidden Markov models
 #include "forward_backward.h"
 #include "reparma.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::List forwardbackwardx(const arma::mat& transition, const arma::cube& emission,

diff --git a/src/internalBackward.cpp b/src/internalBackward.cpp
@@ -1,6 +1,6 @@
 // Internal backward algorithms for HMMs and MHMMs
 #include "forward_backward.h"
-#include <omp.h>
+#include "useomp.h"
 
 void internalBackward(const arma::mat& transition, const arma::cube& emission,
     const arma::ucube& obs, arma::cube& beta, const arma::mat& scales, 

diff --git a/src/internalForward.cpp b/src/internalForward.cpp
@@ -1,7 +1,7 @@
 // Internal forward algorithms for HMMs and MHMMs
 
 #include "forward_backward.h"
-#include <omp.h>
+#include "useomp.h"
 
 void internalForward(const arma::mat& transition_t, const arma::cube& emission, const arma::vec& init,
   const arma::ucube& obs, arma::cube& alpha, arma::mat& scales, unsigned int threads) {

diff --git a/src/logLikHMM.cpp b/src/logLikHMM.cpp
@@ -1,6 +1,6 @@
 // log-likelihood of HMM
 #include <RcppArmadillo.h>
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::NumericVector logLikHMM(const arma::mat& transition, const arma::cube& emission,

diff --git a/src/logLikMixHMM.cpp b/src/logLikMixHMM.cpp
@@ -1,7 +1,7 @@
 // log-likelihood of MHMM using log-space
 #include <RcppArmadillo.h>
 #include "reparma.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::NumericVector logLikMixHMM(const arma::mat& transition, const arma::cube& emission,

diff --git a/src/log_EM.cpp b/src/log_EM.cpp
@@ -2,7 +2,7 @@
 
 #include "log_forward_backward.h"
 #include "logsumexp.h"
-#include <omp.h>
+#include "useomp.h"
 // [[Rcpp::export]]
 Rcpp::List log_EM(const arma::mat& transition_, const arma::cube& emission_, 
   const arma::vec& init_, const arma::ucube& obs, const arma::uvec& nSymbols, 

diff --git a/src/log_EMx.cpp b/src/log_EMx.cpp
@@ -4,7 +4,7 @@
 #include "optcoef.h"
 #include "logsumexp.h"
 #include "reparma.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::List log_EMx(const arma::mat& transition_, const arma::cube& emission_, 

diff --git a/src/log_forwardbackward.cpp b/src/log_forwardbackward.cpp
@@ -1,7 +1,7 @@
 // Forward-backward algorithm for non-mixture hidden Markov models using log-space
 
 #include "log_forward_backward.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::List log_forwardbackward(const arma::mat& transition_, const arma::cube& emission_, 

diff --git a/src/log_forwardbackwardx.cpp b/src/log_forwardbackwardx.cpp
@@ -2,7 +2,7 @@
 
 #include "log_forward_backward.h"
 #include "reparma.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::List log_forwardbackwardx(const arma::mat& transition_, 

diff --git a/src/log_internalBackward.cpp b/src/log_internalBackward.cpp
@@ -2,7 +2,7 @@
 
 #include "forward_backward.h"
 #include "logsumexp.h"
-#include <omp.h>
+#include "useomp.h"
 
 void log_internalBackward(const arma::mat& transition, const arma::cube& emission,
   const arma::ucube& obs, arma::cube& beta, unsigned int threads) {

diff --git a/src/log_internalForward.cpp b/src/log_internalForward.cpp
@@ -2,7 +2,7 @@
 
 #include "forward_backward.h"
 #include "logsumexp.h"
-#include <omp.h>
+#include "useomp.h"
 
 void log_internalForward(const arma::mat& transition, const arma::cube& emission,
   const arma::vec& init, const arma::ucube& obs, arma::cube& alpha, unsigned int threads) {

diff --git a/src/log_logLikHMM.cpp b/src/log_logLikHMM.cpp
@@ -1,7 +1,7 @@
 // log-likelihood of HMM using log-space
 
 #include "logsumexp.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::NumericVector log_logLikHMM(const arma::mat& transition_, const arma::cube& emission_, 

diff --git a/src/log_logLikMixHMM.cpp b/src/log_logLikMixHMM.cpp
@@ -2,7 +2,7 @@
 
 #include "logsumexp.h"
 #include "reparma.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::NumericVector log_logLikMixHMM(arma::mat transition, arma::cube emission, arma::vec init,

diff --git a/src/log_objective.cpp b/src/log_objective.cpp
@@ -2,7 +2,7 @@
 
 #include "log_forward_backward.h"
 #include "logsumexp.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::List log_objective(const arma::mat& transition, const arma::cube& emission,

diff --git a/src/log_objectivex.cpp b/src/log_objectivex.cpp
@@ -3,7 +3,7 @@
 #include "logsumexp.h"
 #include "reparma.h"
 
-#include <omp.h>
+#include "useomp.h"
 // [[Rcpp::export]]
 Rcpp::List log_objectivex(const arma::mat& transition, const arma::cube& emission,
   const arma::vec& init, const arma::ucube& obs, const arma::umat& ANZ,

diff --git a/src/objective.cpp b/src/objective.cpp
@@ -1,7 +1,7 @@
 // log-likelihood and gradients of HMM
 #include "optcoef.h"
 #include "forward_backward.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::List objective(const arma::mat& transition, const arma::cube& emission,

diff --git a/src/objectivex.cpp b/src/objectivex.cpp
@@ -2,7 +2,7 @@
 #include "optcoef.h"
 #include "forward_backward.h"
 #include "reparma.h"
-#include <omp.h>
+#include "useomp.h"
 
 // [[Rcpp::export]]
 Rcpp::List objectivex(const arma::mat& transition, const arma::cube& emission,

diff --git a/src/useomp.h b/src/useomp.h
@@ -0,0 +1,3 @@
+#ifdef _OPENMP
+  #include <omp.h>
+#endif