1. OncoSimulR
  2. src
  3. Makevars
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no longer needed to specify CXX_STD = CXX14

ramon diaz-uriarte (at Phelsuma) authored on 20/02/2023 19:00:22
Showing 1 changed files
src/Makevars
History View file @ 99789c7
... ... 
@@ -6,10 +6,11 @@ CXX11=g++$(VER)
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 ## This is a C++11 package
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 ## but using C++14 leads to faster INSTALL. In my machine:
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+## C++14 is default starting from R-4.1.0
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 ## C++11: 6'30"
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 ## C++14: 4'20"
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 ## C++17: 5'08"
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-CXX_STD = CXX14
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+## CXX_STD = CXX14
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 all: liblandscape.a fl_statistics fl_generate $(SHLIB)
Browse code

3.99.8: unity build

ramon diaz-uriarte (at Phelsuma) authored on 15/09/2022 19:29:51
Showing 1 changed files
src/Makevars
History View file @ 9d183dd
... ... 
@@ -3,31 +3,16 @@ CC=gcc$(VER)
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 CXX=g++$(VER)
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 CXX11=g++$(VER)
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+
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 ## This is a C++11 package
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-## But using C++14 leads to faster INSTALL. In my machine:
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+## but using C++14 leads to faster INSTALL. In my machine:
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 ## C++11: 6'30"
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 ## C++14: 4'20"
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 ## C++17: 5'08"
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 CXX_STD = CXX14
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-# This ain't needed
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-# ONCOSIMUL_SRC = BNB_nr.cpp\
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-# 	BNB_v1.cpp\
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-# 	bnb_common.cpp\
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-# 	new_restrict.cpp\
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-# 	accessible_genotypes.cpp\
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-# 	RcppExports.cpp\
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-# 	OncoSimulR_init.c\
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-# ONCOSIMUL_OBJECTS_TMP=$(ONCOSIMUL_SRC:.cpp=.o)
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-# ONCOSIMUL_OBJECTS=$(ONCOSIMUL_OBJECTS_TMP:.c=.o)
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-
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-# .PHONY: all liblandscape.a
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-# all: $(SHLIB)
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-# all: liblandscape.a $(SHLIB)
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 all: liblandscape.a fl_statistics fl_generate $(SHLIB)
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-## all: liblandscape.a fl_statistics fl_generate fl_genchains $(SHLIB)
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-
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 MAGELLAN_SRC = FitnessLandscape/gamma.c\
... ... 
@@ -47,7 +32,7 @@ MAGELLAN_SRC = FitnessLandscape/gamma.c\
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         FitnessLandscape/decomposition.c\
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         FitnessLandscape/models.c\
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 	FitnessLandscape/verbose.c
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-#        FitnessLandscape/common_drawings.c\ ## I do not use it and gives a warning
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+
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 MAGELLAN_OBJECTS = $(MAGELLAN_SRC:.c=.o)
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 liblandscape.a: $(MAGELLAN_OBJECTS)
... ... 
@@ -59,7 +44,6 @@ liblandscape.a: $(MAGELLAN_OBJECTS)
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 MAGELLAN_LIBS = liblandscape.a
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 MAGELLAN_LIBS_DIR = -L.
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 MAGELLAN_LFLAGS = -llandscape
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-## MAGELLAN_INCLUDE_DIR = -I. -I/FitnessLandscape/.
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 MAGELLAN_INCLUDE_DIR = -I/FitnessLandscape/.
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 MAGELLAN_ALLCFLAGS= -O -Wall
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... ... 
@@ -69,31 +53,5 @@ fl_statistics: FitnessLandscape/main_fl_statistics.c $(MAGELLAN_LIBS)
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 fl_generate: FitnessLandscape/main_fl_generate.c  $(MAGELLAN_LIBS)
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 	$(CC) $(MAGELLAN_ALLCFLAGS) -o $@ $(MAGELLAN_INCLUDE_DIR) $(MAGELLAN_LIBS_DIR) $< $(MAGELLAN_LFLAGS) -lm;
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-# # Do we really need this?
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-# fl_genchains: FitnessLandscape/main_generalizedchains_test.c $(MAGELLAN_LIBS)
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-# 	$(CC) $(MAGELLAN_ALLCFLAGS) -o $@ $(MAGELLAN_INCLUDE_DIR) $(MAGELLAN_LIBS_DIR) $< $(MAGELLAN_LFLAGS) -lm #-g
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-
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-
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-
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-
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-
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-# fl_stats:
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-# 	echo "make fl_statistics in FitnessLandscape/ ..."
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-# 	(cd MAGELLAN; $(MAKE) fl_statistics)
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-
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-# fl_gen:
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-# 	echo "make fl_generate in FitnessLandscape/ ..."
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-# 	(cd MAGELLAN; $(MAKE) fl_generate)
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-
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-# liblandscape:
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-# 	echo "make liblandscape in FitnessLandscape/ ..."
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-# 	(cd MAGELLAN; $(MAKE) liblandscape.a)
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-
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-# magellanall:
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-# 	echo "make all MAGELLAN in FitnessLandscape/ ..."
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-# 	(cd MAGELLAN; $(MAKE) magellanall)
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-# clean:
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-# 	echo "mak clean in FitnessLandscape/ ..."
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-# 	(cd MAGELLAN; $(MAKE) clean)
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Browse code

3.99.7: c++14 and no o3 in win to try faster build

ramon diaz-uriarte (at Phelsuma) authored on 13/09/2022 15:28:36
Showing 1 changed files
src/Makevars
History View file @ 7d0e975
... ... 
@@ -4,7 +4,11 @@ CXX=g++$(VER)
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 CXX11=g++$(VER)
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 ## This is a C++11 package
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-CXX_STD = CXX11
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+## But using C++14 leads to faster INSTALL. In my machine:
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+## C++11: 6'30"
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+## C++14: 4'20"
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+## C++17: 5'08"
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+CXX_STD = CXX14
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 # This ain't needed
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 # ONCOSIMUL_SRC = BNB_nr.cpp\
Browse code

3.99.1: interventions, death with fdf, user variables

ramon diaz-uriarte (at Phelsuma) authored on 25/06/2022 14:24:13
Showing 1 changed files
src/Makevars
History View file @ 79ffadf
... ... 
@@ -1,3 +1,8 @@
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+VER=
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+CC=gcc$(VER)
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+CXX=g++$(VER)
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+CXX11=g++$(VER)
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+
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 ## This is a C++11 package
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 CXX_STD = CXX11
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... ... 
@@ -20,6 +25,7 @@ all: liblandscape.a fl_statistics fl_generate $(SHLIB)
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 ## all: liblandscape.a fl_statistics fl_generate fl_genchains $(SHLIB)
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+
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 MAGELLAN_SRC = FitnessLandscape/gamma.c\
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         FitnessLandscape/landscape.c \
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         FitnessLandscape/random.c\
Browse code

version 2.99.1: frequency-dependent fitness functionality

ramon diaz-uriarte (at Phelsuma) authored on 10/12/2020 11:41:53
Showing 1 changed files
src/Makevars
History View file @ 4068375
... ... 
@@ -86,3 +86,4 @@ fl_generate: FitnessLandscape/main_fl_generate.c  $(MAGELLAN_LIBS)
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 # 	echo "mak clean in FitnessLandscape/ ..."
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 # 	(cd MAGELLAN; $(MAKE) clean)
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+
Browse code

2.17.4

ramon diaz-uriarte (at Phelsuma) authored on 19/12/2019 08:27:20
Showing 1 changed files
src/Makevars
History View file @ 0796b29
... ... 
@@ -35,7 +35,8 @@ MAGELLAN_SRC = FitnessLandscape/gamma.c\
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         FitnessLandscape/summary_statistics.c\
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         FitnessLandscape/epistasis_type.c\
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         FitnessLandscape/decomposition.c\
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-        FitnessLandscape/models.c
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+        FitnessLandscape/models.c\
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+	FitnessLandscape/verbose.c
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 #        FitnessLandscape/common_drawings.c\ ## I do not use it and gives a warning
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 MAGELLAN_OBJECTS = $(MAGELLAN_SRC:.c=.o)
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Browse code

2.15.1: Added MAGELLANs sources and functionality from MAGELLAN

ramon diaz-uriarte (at Phelsuma) authored on 02/07/2019 14:55:40
Showing 1 changed files
src/Makevars
History View file @ fd073de
... ... 
@@ -1,3 +1,87 @@
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 ## This is a C++11 package
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 CXX_STD = CXX11
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-
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+
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+# This ain't needed
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+# ONCOSIMUL_SRC = BNB_nr.cpp\
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+# 	BNB_v1.cpp\
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+# 	bnb_common.cpp\
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+# 	new_restrict.cpp\
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+# 	accessible_genotypes.cpp\
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+# 	RcppExports.cpp\
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+# 	OncoSimulR_init.c\
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+# ONCOSIMUL_OBJECTS_TMP=$(ONCOSIMUL_SRC:.cpp=.o)
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+# ONCOSIMUL_OBJECTS=$(ONCOSIMUL_OBJECTS_TMP:.c=.o)
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+
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+# .PHONY: all liblandscape.a
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+# all: $(SHLIB)
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+# all: liblandscape.a $(SHLIB)
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+
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+all: liblandscape.a fl_statistics fl_generate $(SHLIB)
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+## all: liblandscape.a fl_statistics fl_generate fl_genchains $(SHLIB)
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+
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+
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+MAGELLAN_SRC = FitnessLandscape/gamma.c\
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+        FitnessLandscape/landscape.c \
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+        FitnessLandscape/random.c\
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+        FitnessLandscape/sort.c\
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+        FitnessLandscape/chain.c\
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+        FitnessLandscape/input.c\
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+        FitnessLandscape/genotypes.c\
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+        FitnessLandscape/ordered_pairs.c\
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+        FitnessLandscape/calculus.c\
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+        FitnessLandscape/vector.c\
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+        FitnessLandscape/generalized_chain.c\
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+        FitnessLandscape/LinearAlgebra.c\
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+        FitnessLandscape/summary_statistics.c\
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+        FitnessLandscape/epistasis_type.c\
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+        FitnessLandscape/decomposition.c\
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+        FitnessLandscape/models.c
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+#        FitnessLandscape/common_drawings.c\ ## I do not use it and gives a warning
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+MAGELLAN_OBJECTS = $(MAGELLAN_SRC:.c=.o)
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+
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+liblandscape.a: $(MAGELLAN_OBJECTS)
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+	$(AR) -r $@ $+ ;
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+	$(RANLIB) $@;
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+
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+
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+
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+MAGELLAN_LIBS = liblandscape.a
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+MAGELLAN_LIBS_DIR = -L.
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+MAGELLAN_LFLAGS = -llandscape
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+## MAGELLAN_INCLUDE_DIR = -I. -I/FitnessLandscape/.
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+MAGELLAN_INCLUDE_DIR = -I/FitnessLandscape/.
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+MAGELLAN_ALLCFLAGS= -O -Wall
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+
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+fl_statistics: FitnessLandscape/main_fl_statistics.c $(MAGELLAN_LIBS)
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+	$(CC) $(MAGELLAN_ALLCFLAGS) -o $@ $(MAGELLAN_INCLUDE_DIR) $(MAGELLAN_LIBS_DIR) $< $(MAGELLAN_LFLAGS) -lm;
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+
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+fl_generate: FitnessLandscape/main_fl_generate.c  $(MAGELLAN_LIBS)
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+	$(CC) $(MAGELLAN_ALLCFLAGS) -o $@ $(MAGELLAN_INCLUDE_DIR) $(MAGELLAN_LIBS_DIR) $< $(MAGELLAN_LFLAGS) -lm;
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+
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+# # Do we really need this?
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+# fl_genchains: FitnessLandscape/main_generalizedchains_test.c $(MAGELLAN_LIBS)
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+# 	$(CC) $(MAGELLAN_ALLCFLAGS) -o $@ $(MAGELLAN_INCLUDE_DIR) $(MAGELLAN_LIBS_DIR) $< $(MAGELLAN_LFLAGS) -lm #-g
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+
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+
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+
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+
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+
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+# fl_stats:
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+# 	echo "make fl_statistics in FitnessLandscape/ ..."
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+# 	(cd MAGELLAN; $(MAKE) fl_statistics)
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+
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+# fl_gen:
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+# 	echo "make fl_generate in FitnessLandscape/ ..."
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+# 	(cd MAGELLAN; $(MAKE) fl_generate)
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+
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+# liblandscape:
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+# 	echo "make liblandscape in FitnessLandscape/ ..."
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+# 	(cd MAGELLAN; $(MAKE) liblandscape.a)
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+
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+# magellanall:
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+# 	echo "make all MAGELLAN in FitnessLandscape/ ..."
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+# 	(cd MAGELLAN; $(MAKE) magellanall)
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+# clean:
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+# 	echo "mak clean in FitnessLandscape/ ..."
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+# 	(cd MAGELLAN; $(MAKE) clean)
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+
Browse code

1.9.3: plots, vignette, max warning and win. failure

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@105255 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 19/06/2015 23:36:35
Showing 1 changed files
src/Makevars
History View file @ f79cc8a
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,3 @@
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+## This is a C++11 package
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+CXX_STD = CXX11
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+