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bpp-phyl: Clarify namespace of 'isnan' function. (#13386)

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t-karatsu 2019-10-23 23:36:01 +09:00 committed by Adam J. Stewart
parent 64694dfaf8
commit 6f41987500
2 changed files with 79 additions and 0 deletions
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75
var/spack/repos/builtin/packages/bpp-phyl/clarify_isnan.patch Normal file
View file

@ -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_)

4
var/spack/repos/builtin/packages/bpp-phyl/package.py
View file

@ -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']