diff options
| -rw-r--r-- | biology/lamarc/Makefile | 6 | ||||
| -rw-r--r-- | biology/lamarc/files/patch-src_control_chainmanager.cpp | 11 | ||||
| -rw-r--r-- | biology/lamarc/files/patch-src_tools_mathx.cpp | 11 | ||||
| -rw-r--r-- | biology/lamarc/files/patch-src_tools_stringx.h | 10 | ||||
| -rw-r--r-- | biology/lamarc/files/patch-src_tree_arrangervec.cpp | 11 | ||||
| -rw-r--r-- | biology/lamarc/files/patch-src_tree_collector.cpp | 11 | ||||
| -rw-r--r-- | biology/lamarc/files/patch-src_tree_prior.cpp | 17 |
7 files changed, 69 insertions, 8 deletions
diff --git a/biology/lamarc/Makefile b/biology/lamarc/Makefile index 46f4e102635a..d9758325fdc8 100644 --- a/biology/lamarc/Makefile +++ b/biology/lamarc/Makefile @@ -1,7 +1,7 @@ PORTNAME= lamarc PORTVERSION= 2.1.8 DISTVERSIONSUFFIX= -src -PORTREVISION= 1 +PORTREVISION= 2 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= http://evolution.genetics.washington.edu/lamarc/download/ @@ -12,14 +12,14 @@ WWW= https://evolution.genetics.washington.edu/lamarc/ LICENSE= APACHE20 -BROKEN_FreeBSD_14= fails to compile: no matching function for call to 'make_pair' - USE_CXXSTD= c++98 GNU_CONFIGURE= yes WRKSRC= ${WRKDIR}/${DISTNAME:S,${DISTVERSIONSUFFIX},,} +CXXFLAGS+= -Wno-unused-parameter -Wno-mismatched-tags + PLIST_FILES= bin/${PORTNAME} PORTDOCS= * diff --git a/biology/lamarc/files/patch-src_control_chainmanager.cpp b/biology/lamarc/files/patch-src_control_chainmanager.cpp new file mode 100644 index 000000000000..bf21359154ab --- /dev/null +++ b/biology/lamarc/files/patch-src_control_chainmanager.cpp @@ -0,0 +1,11 @@ +--- src/control/chainmanager.cpp.orig 2025-05-18 23:57:13 UTC ++++ src/control/chainmanager.cpp +@@ -1631,7 +1631,7 @@ vector<pair<double, long int> > ChainManager::SortChai + unsigned long int i; + for (i = 0; i < temps.size(); ++i) + { +- orderedtemps.push_back(make_pair<double, long int>(temps[i].GetTemperature(), i)); ++ orderedtemps.push_back(make_pair(temps[i].GetTemperature(), i)); + } + std::sort(orderedtemps.begin(), orderedtemps.end()); + return orderedtemps; diff --git a/biology/lamarc/files/patch-src_tools_mathx.cpp b/biology/lamarc/files/patch-src_tools_mathx.cpp new file mode 100644 index 000000000000..527dfe4af344 --- /dev/null +++ b/biology/lamarc/files/patch-src_tools_mathx.cpp @@ -0,0 +1,11 @@ +--- src/tools/mathx.cpp.orig 2025-05-19 00:00:29 UTC ++++ src/tools/mathx.cpp +@@ -778,7 +778,7 @@ std::pair<DoubleVec1d, DoubleVec2d> EigenCalculator::E + { + eigvals[i] = a[i][i]; + } +- return std::make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs); ++ return std::make_pair(eigvals, eigvecs); + } // Eigen + + //------------------------------------------------------------------------------------ diff --git a/biology/lamarc/files/patch-src_tools_stringx.h b/biology/lamarc/files/patch-src_tools_stringx.h index d1ded1a7d8da..04019393fbac 100644 --- a/biology/lamarc/files/patch-src_tools_stringx.h +++ b/biology/lamarc/files/patch-src_tools_stringx.h @@ -1,6 +1,6 @@ --- src/tools/stringx.h.orig 2011-04-23 02:02:49 UTC +++ src/tools/stringx.h -@@ -107,6 +107,26 @@ struct CIStringCompare : public std::bin +@@ -107,6 +107,26 @@ bool ciStringEqual(const std::string& s1, const std::s bool ciStringEqual(const std::string& s1, const std::string& s2); @@ -27,10 +27,11 @@ //------------------------------------------------------------------------------------ template <class T> -@@ -188,26 +208,6 @@ bool FromString(const std::string & in, +@@ -187,26 +207,6 @@ DoubleVec1d StringToDoubleVecOrBarf(const std::string& + bool FromString(const std::string & in, method_type& out); DoubleVec1d StringToDoubleVecOrBarf(const std::string& in); - +- -// functions for making xmltags and lines of xml -std::string MakeTag(const std::string& str); -std::string MakeCloseTag(const std::string& str); @@ -50,7 +51,6 @@ -std::string Pretty(long number, int width=DEFWIDTH); -std::string Pretty(unsigned long number, int width=DEFWIDTH); -std::string Pretty(std::string str, int width=DEFWIDTH); -- + bool StringCompare(const std::string&, const char*, long, long); bool StringCompare(const std::string&, const std::string&, long, long); - diff --git a/biology/lamarc/files/patch-src_tree_arrangervec.cpp b/biology/lamarc/files/patch-src_tree_arrangervec.cpp new file mode 100644 index 000000000000..ff3636f3a571 --- /dev/null +++ b/biology/lamarc/files/patch-src_tree_arrangervec.cpp @@ -0,0 +1,11 @@ +--- src/tree/arrangervec.cpp.orig 2025-05-18 23:55:20 UTC ++++ src/tree/arrangervec.cpp +@@ -116,7 +116,7 @@ void ArrangerVec::CopyAllMembers(const ArrangerVec & c + 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)); + } + } + } diff --git a/biology/lamarc/files/patch-src_tree_collector.cpp b/biology/lamarc/files/patch-src_tree_collector.cpp new file mode 100644 index 000000000000..bff56a70b261 --- /dev/null +++ b/biology/lamarc/files/patch-src_tree_collector.cpp @@ -0,0 +1,11 @@ +--- src/tree/collector.cpp.orig 2025-05-18 23:58:39 UTC ++++ src/tree/collector.cpp +@@ -204,7 +204,7 @@ void ParamCollector::AddParamSummary(ForceParameters f + + void ParamCollector::AddParamSummary(ForceParameters fp, long ncopy) + { +- m_paramsum.push_back(make_pair<ForceParameters, long>(fp, ncopy)); ++ m_paramsum.push_back(std::make_pair(fp, ncopy)); + } + + //------------------------------------------------------------------------------------ diff --git a/biology/lamarc/files/patch-src_tree_prior.cpp b/biology/lamarc/files/patch-src_tree_prior.cpp new file mode 100644 index 000000000000..a8dbf7ab04ed --- /dev/null +++ b/biology/lamarc/files/patch-src_tree_prior.cpp @@ -0,0 +1,17 @@ +--- src/tree/prior.cpp.orig 2025-05-18 23:58:05 UTC ++++ src/tree/prior.cpp +@@ -85,12 +85,12 @@ std::pair<double, double> Prior::RandomDraw() const + 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) + |