commit: 71fb540e91fd211248ed97daee867d9bfe77fa4d Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Thu May 5 18:11:32 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Thu May 5 18:11:49 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=71fb540e
sci-biology/allpathslg: replace isnan macro with proper std::isnan function Gentoo-Bug: 580086 Package-Manager: portage-2.2.28 .../allpathslg-52488_remove-namespace-std.patch | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch b/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch index a094c53..56d0406 100644 --- a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch +++ b/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch @@ -890,10 +890,12 @@ https://bugs.gentoo.org/show_bug.cgi?id=568440 bool IsBubbleEdge(int eid, const HyperBasevector& hb, const vec<int>& to_left, --- allpathslg-52488/src/paths/long/VariantReadSupport.cc +++ allpathslg-52488/src/paths/long/VariantReadSupport.cc -@@ -23,6 +23,11 @@ +@@ -23,6 +23,13 @@ #include "paths/long/ReadOriginTracker.h" #include "paths/long/EvalByReads.h" ++#include <cmath> ++ +using std::get; +using std::make_tuple; +using std::ignore; @@ -902,6 +904,24 @@ https://bugs.gentoo.org/show_bug.cgi?id=568440 namespace { void CalcLengthProbSimple(vec<double>&vOut,const double dProbIns_len, const double dProbDel_len, const uint64_t org_length){ const double dProbIns=dProbIns_len; +@@ -158,7 +165,7 @@ + for(uint64_t ff=1;ff<nFlavors;++ff){ + for( size_t ll = 2 ; ll <= get<0>(n_q_len[ff]) ; ++ll){ dFactor /= (long double)(ll); } + } +- if( dFactor==std::numeric_limits<long double>::infinity() || isnan(dFactor) ){ dFactor=1.0; } ++ if( dFactor==std::numeric_limits<long double>::infinity() || std::isnan(dFactor) ){ dFactor=1.0; } + if(verbosity>0) std::cout << "dFactor " << dFactor << std::endl; + + long double dDenom=0.0; +@@ -193,7 +200,7 @@ + } + } + if(verbosity>0) std::cout <<"denom: " << dDenom<< std::endl; +- if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || isnan(dDenom)) return; ++ if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || std::isnan(dDenom)) return; + ForceAssert(dDenom>0); + if(verbosity>0){ + for( uint64_t row=0;row<nFlavors;++row){ --- allpathslg-52488/src/paths/long/VariantReadSupport.h +++ allpathslg-52488/src/paths/long/VariantReadSupport.h @@ -5,6 +5,8 @@
