From 76cdc9ca1d359709c4ac2d4fc0e60503f9d19c99 Mon Sep 17 00:00:00 2001
From: michellepistner <pistner@psu.edu>
Date: Fri, 31 May 2024 12:26:00 -0400
Subject: [PATCH] updating the configure script thanks to ivan

---
 DESCRIPTION  | 12 ++++++------
 configure    | 30 ++++++++++++++++--------------
 configure.ac | 27 +++++++++++++--------------
 3 files changed, 35 insertions(+), 34 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0ec3991..51cfcd5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,14 +3,14 @@ Type: Package
 Title: Bayesian Multinomial Logistic Normal Regression
 Version: 1.1.0
 Date: 2024-05-15
-Authors@R: c(person("Justin", "Silverman", role=c("aut", "cre"),
-                     email = "JustinSilverman@psu.edu"), 
+Authors@R: c(person("Justin", "Silverman", role=c("aut"),
+                     email = "Justin.Silverman@psu.edu"), 
              person("Kim", "Roche", role=("ctb"), 
                      email = "kimberly.roche@duke.edu"),
-             person("Michelle", "Nixon", role=c("aut"), 
-                     email = "pistnerm1@gmail.com"))
-Maintainer: Justin Silverman
-    <JustinSilverman@psu.edu>
+             person("Michelle", "Nixon", role=c("ctb","cre"), 
+                     email = "pistner@psu.edu"))
+Maintainer: Michelle Nixon
+    <pistner@psu.edu>
 Description: Provides methods for fitting and inspection of Bayesian Multinomial Logistic Normal Models using MAP estimation and Laplace Approximation as developed in Silverman et. Al. (2022) <https://www.jmlr.org/papers/v23/19-882.html>. Key functionality is implemented in C++ for scalability. 'fido' replaces the previous package 'stray'.
 License: GPL-3
 URL: https://jsilve24.github.io/fido/
diff --git a/configure b/configure
index 7d7030d..ec25cdb 100755
--- a/configure
+++ b/configure
@@ -3249,20 +3249,22 @@ mkdir -p "${BUILDDIR}"
 owd=$(pwd)
 cd "${BUILDDIR}"
 
-# The configure script:
-cat > test-omp.cpp <<EOF
-#include <omp.h>
-extern "C" void configtest(int * arg) {
-  *arg = omp_get_num_threads();
-}
-EOF
-# Without the following you're relying on the GNU/Linux-like behaviour
-# w.r.t. undefined symbols (see WRE 1.2.1.1):
-cat > Makevars <<EOF
-PKG_CXXFLAGS = \$(SHLIB_OPENMP_CXXFLAGS)
-PKG_LIBS = \$(SHLIB_OPENMP_CXXFLAGS)
-EOF
-R CMD SHLIB test-omp.cpp
+# MPN: These updates were from a (very, very useful) help question posted to r-package-devel
+# Credit goes to Ivan Krylov.
+
+# compile and link the shared object
+"${R_HOME}/bin/R" CMD SHLIB test-omp.cpp
+# load it and use a function from the inside
+"${R_HOME}/bin/Rscript" -e '
+ dyn.load(paste0("test-omp", .Platform$dynlib.ext))
+ .C("configtest", arg = integer(1))$arg
+'
+if test $? -eq 0; then
+ # everything seems to have succeeded
+ openmp_already_works="yes"
+fi
+# let the user know either way
+AC_MSG_RESULT([${openmp_already_works}])
 
 ## Go back home.
 cd "${owd}"
diff --git a/configure.ac b/configure.ac
index 6f28523..2ee601c 100644
--- a/configure.ac
+++ b/configure.ac
@@ -46,20 +46,19 @@ mkdir -p "${BUILDDIR}"
 owd=$(pwd)
 cd "${BUILDDIR}"
 
-# The configure script:
-cat > test-omp.cpp <<EOF
-#include <omp.h>
-extern "C" void configtest(int * arg) {
-  *arg = omp_get_num_threads();
-}
-EOF
-# Without the following you're relying on the GNU/Linux-like behaviour
-# w.r.t. undefined symbols (see WRE 1.2.1.1):
-cat > Makevars <<EOF
-PKG_CXXFLAGS = \$(SHLIB_OPENMP_CXXFLAGS)
-PKG_LIBS = \$(SHLIB_OPENMP_CXXFLAGS)
-EOF
-R CMD SHLIB test-omp.cpp
+# compile and link the shared object
+"${R_HOME}/bin/R" CMD SHLIB test-omp.cpp
+# load it and use a function from the inside
+"${R_HOME}/bin/Rscript" -e '
+ dyn.load(paste0("test-omp", .Platform$dynlib.ext))
+ .C("configtest", arg = integer(1))$arg
+'
+if test $? -eq 0; then
+ # everything seems to have succeeded
+ openmp_already_works="yes"
+fi
+# let the user know either way
+AC_MSG_RESULT([${openmp_already_works}])
 
 ## Go back home.
 cd "${owd}"