From 6f41987500cf9bd4b9b28dd1f282326d0a3d7323 Mon Sep 17 00:00:00 2001
From: t-karatsu <49965247+t-karatsu@users.noreply.github.com>
Date: Wed, 23 Oct 2019 23:36:01 +0900
Subject: [PATCH] bpp-phyl: Clarify namespace of 'isnan' function. (#13386)

---
 .../packages/bpp-phyl/clarify_isnan.patch     | 75 +++++++++++++++++++
 .../builtin/packages/bpp-phyl/package.py      |  4 +
 2 files changed, 79 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bpp-phyl/clarify_isnan.patch

diff --git a/var/spack/repos/builtin/packages/bpp-phyl/clarify_isnan.patch b/var/spack/repos/builtin/packages/bpp-phyl/clarify_isnan.patch
new file mode 100644
index 0000000000..705e4ead97
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bpp-phyl/clarify_isnan.patch
@@ -0,0 +1,75 @@
+diff -ur bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/DecompositionReward.cpp bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/DecompositionReward.cpp
+--- bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/DecompositionReward.cpp	2019-10-21 14:56:59.567938605 +0900
++++ bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/DecompositionReward.cpp	2019-10-21 14:59:43.645224219 +0900
+@@ -137,7 +137,7 @@
+   for (size_t j = 0; j < nbStates_; j++) {
+     for (size_t k = 0; k < nbStates_; k++) {
+       rewards_(j, k) /= P(j, k);
+-      if (isnan(rewards_(j, k)))
++      if (std::isnan(rewards_(j, k)))
+         rewards_(j, k) = 0.;
+     }
+   }
+diff -ur bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp
+--- bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp	2019-10-21 14:56:59.567938605 +0900
++++ bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp	2019-10-21 15:00:02.147173408 +0900
+@@ -166,7 +166,7 @@
+     for (size_t j = 0; j < nbStates_; j++) {
+       for (size_t k = 0; k < nbStates_; k++) {
+         counts_[i](j, k) /= P(j, k);
+-        if (isnan(counts_[i](j, k)) || counts_[i](j, k) < 0.) {
++        if (std::isnan(counts_[i](j, k)) || counts_[i](j, k) < 0.) {
+           counts_[i](j, k) = 0.;
+         //Weights:
+         if (weights_)
+diff -ur bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp
+--- bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp	2019-10-21 14:56:59.567938605 +0900
++++ bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp	2019-10-21 15:00:45.601751367 +0900
+@@ -1427,7 +1427,7 @@
+       for (size_t t = 0; t < nbTypes; ++t)
+       {
+         tmp[t] = (*mapping)(mapping->getNodeIndex(ids[k]), i, t);
+-        error = isnan(tmp[t]);
++        error = std::isnan(tmp[t]);
+         if (error)
+           goto ERROR;
+         s += tmp[t];
+@@ -1509,7 +1509,7 @@
+       for (size_t t = 0; t < nbTypes; ++t)
+       {
+         tmp[t] = (*mapping)(mapping->getNodeIndex(ids[k]), i, t);
+-        error = isnan(tmp[t]);
++        error = std::isnan(tmp[t]);
+         if (error)
+           goto ERROR;
+         s += tmp[t];
+@@ -1609,7 +1609,7 @@
+       for (size_t i = 0; i < nbSites; ++i)
+       {
+         double tmp = (*mapping)(k, i);
+-        if (isnan(tmp))
++        if (std::isnan(tmp))
+         {
+           if (verbose)
+             ApplicationTools::displayWarning("On branch " + TextTools::toString(ids[k]) + ", reward for type " + reg.getTypeName(nbt + 1) + " could not be computed.");
+@@ -1689,7 +1689,7 @@
+           for (size_t i = 0; i < nbSites; ++i)
+           {
+             double tmp = (*mapping)(mapping->getNodeIndex(mids[k]), i);
+-            if (isnan(tmp))
++            if (std::isnan(tmp))
+             {
+               if (verbose)
+                 ApplicationTools::displayWarning("On branch " + TextTools::toString(mids[k]) + ", reward for type " + reg.getTypeName(nbt + 1) + " could not be computed.");
+diff -ur bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp
+--- bpp-phyl-2.2.0.back/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp	2019-10-21 14:56:59.567938605 +0900
++++ bpp-phyl-2.2.0/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp	2019-10-21 15:01:30.276461683 +0900
+@@ -163,7 +163,7 @@
+     for (size_t j = 0; j < nbStates_; j++) {
+       for(size_t k = 0; k < nbStates_; k++) {
+         counts_[i](j, k) /= P(j, k);
+-        if (isnan(counts_[i](j, k)) || counts_[i](j, k) < 0.)
++        if (std::isnan(counts_[i](j, k)) || counts_[i](j, k) < 0.)
+           counts_[i](j, k) = 0;
+         //Weights:
+         if (weights_)
diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py
index f48889a882..e2b8f0588a 100644
--- a/var/spack/repos/builtin/packages/bpp-phyl/package.py
+++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py
@@ -18,5 +18,9 @@ class BppPhyl(CMakePackage):
     depends_on('bpp-core')
     depends_on('bpp-seq')
 
+    # Clarify isnan's namespace, because Fujitsu compiler can't
+    # resolve ambiguous of 'isnan' function.
+    patch('clarify_isnan.patch', when='%fj')
+
     def cmake_args(self):
         return ['-DBUILD_TESTING=FALSE']