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bpp-suite: Clarify 'isinf' function's namespace. (#13777)

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t-karatsu 2019-11-21 07:52:44 +09:00 committed by Adam J. Stewart
parent ad4986be94
commit af9281b843
2 changed files with 94 additions and 0 deletions
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90
var/spack/repos/builtin/packages/bpp-suite/clarify_isinf.patch Normal file
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@ -0,0 +1,90 @@
diff -ur spack-src.org/bppSuite/bppAncestor.cpp spack-src/bppSuite/bppAncestor.cpp
--- spack-src.org/bppSuite/bppAncestor.cpp 2019-11-18 15:59:34.786164416 +0900
+++ spack-src/bppSuite/bppAncestor.cpp 2019-11-18 16:26:25.385749490 +0900
@@ -237,7 +237,7 @@
delete tree;
double logL = tl->getValue();
- if (isinf(logL))
+ if (std::isinf(logL))
{
// This may be due to null branch lengths, leading to null likelihood!
ApplicationTools::displayWarning("!!! Warning!!! Likelihood is zero.");
@@ -251,7 +251,7 @@
tl->matchParametersValues(pl);
logL = tl->getValue();
}
- if (isinf(logL))
+ if (std::isinf(logL))
{
ApplicationTools::displayError("!!! Unexpected likelihood == 0.");
ApplicationTools::displayError("!!! Looking at each site:");
diff -ur spack-src.org/bppSuite/bppML.cpp spack-src/bppSuite/bppML.cpp
--- spack-src.org/bppSuite/bppML.cpp 2019-11-18 15:59:34.786164416 +0900
+++ spack-src/bppSuite/bppML.cpp 2019-11-18 16:29:09.373021202 +0900
@@ -425,7 +425,7 @@
//Check initial likelihood:
double logL = tl->getValue();
- if (isinf(logL))
+ if (std::isinf(logL))
{
// This may be due to null branch lengths, leading to null likelihood!
ApplicationTools::displayWarning("!!! Warning!!! Initial likelihood is zero.");
@@ -440,7 +440,7 @@
logL = tl->getValue();
}
ApplicationTools::displayResult("Initial log likelihood", TextTools::toString(-logL, 15));
- if (isinf(logL))
+ if (std::isinf(logL))
{
ApplicationTools::displayError("!!! Unexpected initial likelihood == 0.");
if (codonAlphabet)
@@ -448,7 +448,7 @@
bool f = false;
size_t s;
for (size_t i = 0; i < sites->getNumberOfSites(); i++) {
- if (isinf(tl->getLogLikelihoodForASite(i))) {
+ if (std::isinf(tl->getLogLikelihoodForASite(i))) {
const Site& site = sites->getSite(i);
s = site.size();
for (size_t j = 0; j < s; j++) {
@@ -477,7 +477,7 @@
} else {
ApplicationTools::displayBooleanResult("Saturated site removal enabled", true);
for (size_t i = sites->getNumberOfSites(); i > 0; --i) {
- if (isinf(tl->getLogLikelihoodForASite(i - 1))) {
+ if (std::isinf(tl->getLogLikelihoodForASite(i - 1))) {
ApplicationTools::displayResult("Ignore saturated site", sites->getSite(i - 1).getPosition());
sites->deleteSite(i - 1);
}
@@ -486,7 +486,7 @@
tl->setData(*sites);
tl->initialize();
logL = tl->getValue();
- if (isinf(logL)) {
+ if (std::isinf(logL)) {
throw Exception("Likelihood is still 0 after saturated sites are removed! Looks like a bug...");
}
ApplicationTools::displayResult("Initial log likelihood", TextTools::toString(-logL, 15));
diff -ur spack-src.org/bppSuite/bppMixedLikelihoods.cpp spack-src/bppSuite/bppMixedLikelihoods.cpp
--- spack-src.org/bppSuite/bppMixedLikelihoods.cpp 2019-11-18 15:59:34.786164416 +0900
+++ spack-src/bppSuite/bppMixedLikelihoods.cpp 2019-11-18 16:26:48.338168188 +0900
@@ -220,7 +220,7 @@
tl->initialize();
double logL = tl->getValue();
- if (isinf(logL))
+ if (std::isinf(logL))
{
// This may be due to null branch lengths, leading to null likelihood!
ApplicationTools::displayWarning("!!! Warning!!! Likelihood is zero.");
@@ -235,7 +235,7 @@
tl->matchParametersValues(pl);
logL = tl->getValue();
}
- if (isinf(logL))
+ if (std::isinf(logL))
{
ApplicationTools::displayError("!!! Unexpected likelihood == 0.");
ApplicationTools::displayError("!!! Looking at each site:");

4
var/spack/repos/builtin/packages/bpp-suite/package.py
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@ -20,3 +20,7 @@ class BppSuite(CMakePackage):
depends_on('bpp-core')
depends_on('bpp-seq')
depends_on('bpp-phyl')
# Clarify isinf's namespace, because Fujitsu compiler can't
# resolve ambiguous of 'isinf' function.
patch('clarify_isinf.patch', when='%fj')