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:");