diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/bpp-core/clarify_isnan.patch | 42 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/bpp-core/package.py | 4 |
2 files changed, 46 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/bpp-core/clarify_isnan.patch b/var/spack/repos/builtin/packages/bpp-core/clarify_isnan.patch new file mode 100644 index 0000000000..6038c15e42 --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-core/clarify_isnan.patch @@ -0,0 +1,42 @@ +diff -ur bpp-core-2.2.0_org/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp bpp-core-2.2.0/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp +--- bpp-core-2.2.0_org/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp 2019-10-18 14:13:47.041015700 +0900 ++++ bpp-core-2.2.0/src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp 2019-10-18 15:32:41.888978173 +0900 +@@ -53,7 +53,7 @@ + function2_->enableSecondOrderDerivatives(false); + function_->setParameters(parameters); + f2_ = function_->getValue(); +- if ((abs(f2_) >= NumConstants::VERY_BIG()) || isnan(f2_)) ++ if ((abs(f2_) >= NumConstants::VERY_BIG()) || std::isnan(f2_)) + { + for (size_t i = 0; i < variables_.size(); ++i) + { +@@ -103,7 +103,7 @@ + + p = p.subList(0); + f1_ = function_->getValue(); +- if ((abs(f1_) >= NumConstants::VERY_BIG()) || isnan(f1_)) ++ if ((abs(f1_) >= NumConstants::VERY_BIG()) || std::isnan(f1_)) + throw ConstraintException("f1_ too large", &p[0], f1_); + else + hf1 = h; +@@ -137,7 +137,7 @@ + + p = p.subList(0); + f3_ = function_->getValue(); +- if ((abs(f3_) >= NumConstants::VERY_BIG()) || isnan(f3_)) ++ if ((abs(f3_) >= NumConstants::VERY_BIG()) || std::isnan(f3_)) + throw ConstraintException("f3_ too large", &p[0], f3_); + else + hf3 = h; +diff -ur bpp-core-2.2.0_org/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp bpp-core-2.2.0/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp +--- bpp-core-2.2.0_org/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp 2019-10-18 14:13:47.051016751 +0900 ++++ bpp-core-2.2.0/src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp 2019-10-18 15:40:33.218550564 +0900 +@@ -124,7 +124,7 @@ + size_t ii = i * nbStates_; + for (size_t j = 0; j < nbStates_; j++) { + trans[ii + j] = transitionMatrix_->Pij(j, i); +- if (isnan(trans[ii + j])) ++ if (std::isnan(trans[ii + j])) + throw Exception("RescaledHmmLikelihood::computeForward_. NaN transition probability"); + if (trans[ii + j] < 0) + throw Exception("RescaledHmmLikelihood::computeForward_. Negative transition probability: " + TextTools::toString(trans[ii + j])); diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py index da9473e2ae..86326ccc1b 100644 --- a/var/spack/repos/builtin/packages/bpp-core/package.py +++ b/var/spack/repos/builtin/packages/bpp-core/package.py @@ -16,5 +16,9 @@ class BppCore(CMakePackage): depends_on('cmake@2.6:', type='build') + # 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'] |