Attachment 260525 Details for Bug 286917 – Git patch to unbreak biology/lamarc on FreeBSD 14+

[patch] Git patch to unbreak biology/lamarc on FreeBSD 14+

0001-biology-lamarc-unbreak-on-FreeBSD-14.patch (text/plain), 6.95 KB, created by Hayzam Sherif on 2025-05-19 00:22:06 UTC

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Creator: Hayzam Sherif

Created: 2025-05-19 00:22:06 UTC

Size: 6.95 KB

patch

obsolete

>From 524c7a8cf9f8802e8b81a65d728827d8de158966 Mon Sep 17 00:00:00 2001
>From: hayzamjs <hayzam@alchemilla.io>
>Date: Mon, 19 May 2025 04:17:48 +0400
>Subject: [PATCH] biology/lamarc: unbreak on FreeBSD 14+
>
>Fix build with Clang 16+ by removing explicit template arguments from
>std::make_pair used with lvalues, which caused build errors.
>
>While here:
>- Regenerated patch-src_tools_stringx.h with consistent offsets
>---
> biology/lamarc/Makefile                         |  2 --
> .../files/patch-src_control_chainmanager.cpp    | 11 +++++++++++
> biology/lamarc/files/patch-src_tools_mathx.cpp  | 11 +++++++++++
> biology/lamarc/files/patch-src_tools_stringx.h  | 10 +++++-----
> .../lamarc/files/patch-src_tree_arrangervec.cpp | 11 +++++++++++
> .../lamarc/files/patch-src_tree_collector.cpp   | 11 +++++++++++
> biology/lamarc/files/patch-src_tree_prior.cpp   | 17 +++++++++++++++++
> 7 files changed, 66 insertions(+), 7 deletions(-)
> create mode 100644 biology/lamarc/files/patch-src_control_chainmanager.cpp
> create mode 100644 biology/lamarc/files/patch-src_tools_mathx.cpp
> create mode 100644 biology/lamarc/files/patch-src_tree_arrangervec.cpp
> create mode 100644 biology/lamarc/files/patch-src_tree_collector.cpp
> create mode 100644 biology/lamarc/files/patch-src_tree_prior.cpp
>
>diff --git a/biology/lamarc/Makefile b/biology/lamarc/Makefile
>index 46f4e10263..33ecc2c9c6 100644
>--- a/biology/lamarc/Makefile
>+++ b/biology/lamarc/Makefile
>@@ -12,8 +12,6 @@ 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
>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 0000000000..bf21359154
>--- /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 0000000000..527dfe4af3
>--- /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 d1ded1a7d8..04019393fb 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 0000000000..ff3636f3a5
>--- /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 0000000000..bff56a70b2
>--- /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 0000000000..a8dbf7ab04
>--- /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) +
>-- 
>2.48.1
>

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Attachments on bug 286917: 260525