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commit d266c46da17076f8dfbdd5bbf2ff27807e4f5649 Author: Gert Wollny <g...@debian.org> Date: Tue Dec 5 09:05:10 2017 +0100 Update patched to make it compile with gcc-7 --- debian/patches/gcc-7.patch | 114 +++++++++++++++++++++++++++++++++++++++++++- debian/patches/limits.patch | 11 +++++ 2 files changed, 124 insertions(+), 1 deletion(-) diff --git a/debian/patches/gcc-7.patch b/debian/patches/gcc-7.patch index 6623324..9ae6f91 100644 --- a/debian/patches/gcc-7.patch +++ b/debian/patches/gcc-7.patch @@ -4,7 +4,7 @@ Description: make_pair doesn't require the explicite type specification --- a/src/tools/mathx.cpp +++ b/src/tools/mathx.cpp -@@ -778,7 +778,7 @@ pair<DoubleVec1d, DoubleVec2d> EigenCalc +@@ -778,7 +778,7 @@ { eigvals[i] = a[i][i]; } @@ -13,3 +13,115 @@ Description: make_pair doesn't require the explicite type specification } // Eigen //------------------------------------------------------------------------------------ +--- a/src/tree/argtree.cpp ++++ b/src/tree/argtree.cpp +@@ -371,7 +371,7 @@ + if (forcefound) + { + // add to target map array +- Branch_ptr nullptr; ++ Branch_ptr null_ptr; + if (recfound) + { + // recombination case - returns a pair of branches +@@ -388,7 +388,7 @@ + else + { + // everything else +- targetpair p = make_pair(recbranches.first, nullptr); ++ targetpair p = make_pair(recbranches.first, null_ptr); + targetmap.insert(make_pair(argedges[edge].GetSource(), p)); + } + +@@ -404,7 +404,7 @@ + else + { + // everything else +- targetpair q = make_pair(recbranches.second, nullptr); ++ targetpair q = make_pair(recbranches.second, null_ptr); + targetmap.insert(make_pair(argedges[edge+1].GetSource(), q)); + } + } +@@ -421,7 +421,7 @@ + else + { + // everything else +- targetpair p = make_pair(newbranch, nullptr); ++ targetpair p = make_pair(newbranch, null_ptr); + targetmap.insert(make_pair(argedges[edge].GetSource(), p)); + } + } +--- a/src/tree/arrangervec.cpp ++++ b/src/tree/arrangervec.cpp +@@ -122,7 +122,7 @@ + for(it = cp.arrangers.begin(); it != cp.arrangers.end(); it++) + { + Arranger* arr = it->second->Clone(); +- arrangers.insert(std::make_pair<string, Arranger*>(arr->GetName(), arr)); ++ arrangers.insert(std::make_pair(arr->GetName(), arr)); + } + } + } +--- a/src/tree/collector.cpp ++++ b/src/tree/collector.cpp +@@ -205,7 +205,7 @@ + + void ParamCollector::AddParamSummary(ForceParameters fp, long ncopy) + { +- m_paramsum.push_back(make_pair<ForceParameters, long>(fp, ncopy)); ++ m_paramsum.push_back(make_pair(fp, ncopy)); + } + + //------------------------------------------------------------------------------------ +--- a/src/tree/prior.cpp ++++ b/src/tree/prior.cpp +@@ -85,12 +85,12 @@ + case LINEAR: + newparam = rnd.Float() * (m_upperbound - m_lowerbound) + m_lowerbound; + newlnparam = log(newparam); +- return std::make_pair<double, double>(newparam, newlnparam); ++ return std::make_pair(newparam, newlnparam); + break; + case LOGARITHMIC: + newlnparam = rnd.Float() * (m_lnupper - m_lnlower) + m_lnlower; + newparam = exp(newlnparam); +- return std::make_pair<double, double>(newparam, newlnparam); ++ return std::make_pair(newparam, newlnparam); + break; + } + string e = "Unknown prior type " + ToString(m_priortype) + +@@ -117,7 +117,7 @@ + { + newparam = 2.0 * m_upperbound - newparam; + } +- return std::make_pair<double,double>(newparam, log(newparam)); ++ return std::make_pair(newparam, log(newparam)); + break; + case LOGARITHMIC: + string e = "Cannot use prior type " + ToString(m_priortype) + +@@ -135,7 +135,7 @@ + std::pair<double, double> Prior::RandomDrawWithinBounds(double lower, double upper) const + { + Random& rnd = registry.GetRandom(); +- double newparam, newlnparam; ++ double newparam = 0, newlnparam = 0; + double lowbound = std::max(m_lowerbound, lower); + double upbound = std::min(m_upperbound, upper); + switch (m_priortype) +@@ -143,15 +143,14 @@ + case LINEAR: + newparam = rnd.Float() * (upbound - lowbound) + lowbound; + newlnparam = log(newparam); +- return std::make_pair<double, double>(newparam, newlnparam); + break; + case LOGARITHMIC: + lowbound = log(lowbound); + upbound = log(upbound); + newlnparam = rnd.Float() * (upbound - lowbound) + lowbound; + newparam = exp(newlnparam); +- return std::make_pair<double, double>(newparam, newlnparam); + break; + } ++ return std::make_pair(newparam, newlnparam); + + } // RandomDrawWithinBounds diff --git a/debian/patches/limits.patch b/debian/patches/limits.patch index b79a557..ca9ae2a 100644 --- a/debian/patches/limits.patch +++ b/debian/patches/limits.patch @@ -12,3 +12,14 @@ Description: Add missing climits // NOTE: older versions required including <direct.h> here and // using _getcwd() below for MSWINDOWS compiles +--- a/src/xml/tixml_base.cpp ++++ b/src/xml/tixml_base.cpp +@@ -13,6 +13,8 @@ + #include "tinyxml.h" + #include "tixml_base.h" + ++#include <climits> ++ + const std::string tibasestr::EXTRA_TAG_0 = "incorrect xml: extra tag \""; + const std::string tibasestr::EXTRA_TAG_1 = "\"."; + const std::string tibasestr::MISSING_TAG_0 = "incorrect xml: missing tag \""; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/lamarc.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit