[lilac] updated to 1.2.1-7

3 files changed, 89 insertions, 10 deletions

diff --git a/.SRCINFO b/.SRCINFO
index d757f9ee5abd..cdd45b085f38 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = revbayes
 	pkgdesc = Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language https://doi.org/10.1093/sysbio/syw021
-	pkgver = 1.2.0
-	pkgrel = 4
+	pkgver = 1.2.1
+	pkgrel = 7
 	url = https://github.com/revbayes/revbayes
 	arch = x86_64
 	license = GPL3
@@ -15,7 +15,9 @@ pkgbase = revbayes
 	depends = openlibm
 	conflicts = lrzsz
 	conflicts = revbayes-mpi
-	source = git+https://github.com/revbayes/revbayes.git#tag=v1.2.0
+	source = git+https://github.com/revbayes/revbayes.git#tag=v1.2.1
+	source = rb.patch
 	md5sums = SKIP
+	md5sums = f5af0159704f049f8269584883bcaa80
 
 pkgname = revbayes
diff --git a/PKGBUILD b/PKGBUILD
index 6f526e77a962..5dece061e92a 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,25 +1,31 @@
 pkgname=revbayes
-pkgver=1.2.0
-pkgrel=4
+pkgver=1.2.1
+pkgrel=7
 pkgdesc="Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language https://doi.org/10.1093/sysbio/syw021"
 arch=(x86_64)
 url="https://github.com/revbayes/revbayes"
 license=(GPL3)
 depends=('gcc-libs' 'boost-libs' 'openlibm')
 makedepends=('boost' 'meson' 'ninja' 'cmake' 'git')
-source=("git+$url.git#tag=v$pkgver")
+source=("git+$url.git#tag=v$pkgver"
+	"rb.patch")
 conflicts=('lrzsz' 'revbayes-mpi')
-md5sums=('SKIP')
+md5sums=('SKIP'
+         'f5af0159704f049f8269584883bcaa80')
 
 prepare() {
   cd $srcdir/$pkgname
+  # fix lib issue
+  patch -p1 < $srcdir/rb.patch  
+
   git submodule update --init --recursive
   ./projects/meson/generate.sh
 }
 
 build() {
   cd $srcdir/$pkgname
-  arch-meson build
+  CXXFLAGS="${CXXFLAGS} -std=c++14" arch-meson build \
+  --buildtype      release
   ninja -C build
 }
 
@@ -27,5 +33,3 @@ package() {
   cd $srcdir/$pkgname
   DESTDIR="${pkgdir}" ninja -C build install
 }
-
-
diff --git a/rb.patch b/rb.patch
new file mode 100644
index 000000000000..e23cd74436dd
--- /dev/null
+++ b/rb.patch
@@ -0,0 +1,73 @@
+From bbae33847c4dc24ffbd3bab2afceb4e3e0bbe757 Mon Sep 17 00:00:00 2001
+From: Kuoi <kuoi@bioarchlinux.org>
+Date: Sat, 24 Dec 2022 23:58:29 +0800
+Subject: [PATCH 1/3] add memory lib
+
+---
+ src/revlanguage/functions/UserFunction.cpp | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/revlanguage/functions/UserFunction.cpp b/src/revlanguage/functions/UserFunction.cpp
+index fe7a958ba0..d7ffe11ea4 100644
+--- a/src/revlanguage/functions/UserFunction.cpp
++++ b/src/revlanguage/functions/UserFunction.cpp
+@@ -10,6 +10,7 @@
+ #include "UserFunction.h"
+ #include "UserFunctionDef.h"
+ #include "Workspace.h"
++#include <memory>
+ #include "Argument.h"
+ #include "Environment.h"
+ #include "RevObject.h"
+
+From ad3f390b67a88923dd39702560510ea91480da77 Mon Sep 17 00:00:00 2001
+From: Kuoi <kuoi@bioarchlinux.org>
+Date: Sun, 25 Dec 2022 00:25:42 +0800
+Subject: [PATCH 2/3] add memory
+
+---
+ src/revlanguage/workspace/RevVariable.cpp | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/revlanguage/workspace/RevVariable.cpp b/src/revlanguage/workspace/RevVariable.cpp
+index 0736ac9663..ded40ee106 100644
+--- a/src/revlanguage/workspace/RevVariable.cpp
++++ b/src/revlanguage/workspace/RevVariable.cpp
+@@ -2,6 +2,7 @@
+ #include <string>
+ #include <sstream>
+ #include <vector>
++#include <memory>
+ 
+ #include "Argument.h"
+ #include "RbException.h"
+
+From 8c78d8a84d3dd1fa57f765ebfa1332de37c7a315 Mon Sep 17 00:00:00 2001
+From: Kuoi <kuoi@bioarchlinux.org>
+Date: Sun, 25 Dec 2022 00:26:27 +0800
+Subject: [PATCH 3/3] adjust position
+
+---
+ src/revlanguage/functions/UserFunction.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/revlanguage/functions/UserFunction.cpp b/src/revlanguage/functions/UserFunction.cpp
+index d7ffe11ea4..33961156cc 100644
+--- a/src/revlanguage/functions/UserFunction.cpp
++++ b/src/revlanguage/functions/UserFunction.cpp
+@@ -3,6 +3,7 @@
+ #include <list>
+ #include <string>
+ #include <vector>
++#include <memory>
+ 
+ #include "RbException.h"
+ #include "Signals.h"
+@@ -10,7 +11,6 @@
+ #include "UserFunction.h"
+ #include "UserFunctionDef.h"
+ #include "Workspace.h"
+-#include <memory>
+ #include "Argument.h"
+ #include "Environment.h"
+ #include "RevObject.h"