From cec6c09b63754e20aff056459be92e7e6dc435af Mon Sep 17 00:00:00 2001
From: Chi Zhang <zhangchicool@gmail.com>
Date: Mon, 6 Apr 2015 14:38:18 +0000
Subject: [PATCH] apply patch for configure --prefix option

---
 src/Makefile.in | 17 ++++++++++-------
 src/utils.c     | 16 ++++++++--------
 src/utils.h     |  1 -
 3 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/src/Makefile.in b/src/Makefile.in
index c1d08325..5a9e4042 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -1,10 +1,12 @@
-srcdir    = @srcdir@
-RM        = rm
-CC        = @CC@
-CFLAGS    = @CFLAGS@ -DUSECONFIG_H
-LDFLAGS   = @LDFLAGS@ -lm
-INSTALL   = @INSTALL@
-BINDIR    = /usr/local/bin
+SRCDIR       = @srcdir@
+RM           = rm
+CC           = @CC@
+CFLAGS       = @CFLAGS@ -DUSECONFIG_H
+LDFLAGS      = @LDFLAGS@ -lm
+INSTALL      = @INSTALL@
+prefix      ?= @prefix@
+exec_prefix ?= @exec_prefix@
+BINDIR      ?= @bindir@
 
 SRC       = bayes.c command.c model.c mcmc.c likelihood.c proposal.c sumpt.c utils.c mbbeagle.c best.c
 OBJECTS   = bayes.o command.o model.o mcmc.o likelihood.o proposal.o sumpt.o utils.o mbbeagle.o best.o
@@ -16,6 +18,7 @@ mb: $(OBJECTS)
 	$(CC) $(CFLAGS) -o $@ $^ $(LDFLAGS)
 
 install: $(PROGS)
+	mkdir -p $(BINDIR)
 	$(INSTALL) -m 755 $(PROGS) $(BINDIR)
 
 clean:
diff --git a/src/utils.c b/src/utils.c
index 63937865..071ffae9 100644
--- a/src/utils.c
+++ b/src/utils.c
@@ -12622,7 +12622,7 @@ MrBFlt LnPriorProbLognormal (MrBFlt val, MrBFlt *params)
 
     z = (log(val) - params[0]) / params[1];
 
-    return -log(params[1] * val * sqrt(2.0 * PI)) - z * z / 2.0;
+    return - log(params[1] * val * sqrt(2.0 * PI)) - z * z / 2.0;
 }
 
 
@@ -12636,7 +12636,7 @@ MrBFlt LnPriorProbLognormal_Param_Mean_Sd (MrBFlt val, MrBFlt *params)
 
     z= (log(val) - mean_log) / sd_log;
 
-    return -log(sd_log * val * sqrt(2.0 * PI)) - z * z / 2.0;
+    return - log(sd_log * val * sqrt(2.0 * PI)) - z * z / 2.0;
 }
 
 
@@ -12647,7 +12647,7 @@ MrBFlt LnPriorProbNormal (MrBFlt val, MrBFlt *params)
 
     z = (val - params[0]) / params[1];
 
-    return -log(params[1] * sqrt(2.0 * PI)) - z * z / 2.0;
+    return - log(params[1] * sqrt(2.0 * PI)) - z * z / 2.0;
 }
 
 
@@ -12710,7 +12710,7 @@ MrBFlt LnPriorProbOffsetLognormal (MrBFlt val, MrBFlt *params)
 
     z = (log(x) - mean_log) / sd_log;
 
-    return -log(sd_log * x * sqrt(2.0 * PI)) - z * z / 2.0;
+    return - log(sd_log * x * sqrt(2.0 * PI)) - z * z / 2.0;
 }
 
 
@@ -12727,7 +12727,7 @@ MrBFlt LnPriorProbOffsetLognormal_Param_Offset_Mean_Sd (MrBFlt val, MrBFlt *para
 
     z = (log(x) - mean_log) / sd_log;
 
-    return -log(sd_log * x * sqrt(2.0 * PI)) - z * z / 2.0;
+    return - log(sd_log * x * sqrt(2.0 * PI)) - z * z / 2.0;
 }
 
 
@@ -12741,7 +12741,7 @@ MrBFlt LnPriorProbTruncatedNormal (MrBFlt val, MrBFlt *params)
     z_0 = (0.0 - params[0]) / params[1];
     normConst = CdfNormal(z_0);
 
-    return -log(params[1] * sqrt(2.0 * PI)) - z * z / 2.0 - log(normConst);
+    return - log(params[1] * sqrt(2.0 * PI)) - z * z / 2.0 - log(normConst);
 }
 
 
@@ -12755,14 +12755,14 @@ MrBFlt LnPriorProbTruncatedNormal_Param_Trunc_Mean_Sd (MrBFlt val, MrBFlt *param
     z_trunc = (params[0] - params[1]) / params[2];
     normConst = CdfNormal(z_trunc);
 
-    return -log(params[2] * sqrt(2.0 * PI)) - z * z / 2.0 - log(normConst);
+    return - log(params[2] * sqrt(2.0 * PI)) - z * z / 2.0 - log(normConst);
 }
 
 
 /* Calculate probability of a realization for uniform random variable */
 MrBFlt LnPriorProbUniform (MrBFlt val, MrBFlt *params)
 {
-    return -log(params[1] - params[0]);
+    return - log(params[1] - params[0]);
     MrBayesPrint ("%lf", val); /* just because I am tired of seeing the unused parameter error msg */
 }
 
diff --git a/src/utils.h b/src/utils.h
index e8fda800..d7a1dfe4 100644
--- a/src/utils.h
+++ b/src/utils.h
@@ -7,7 +7,6 @@ struct complex
     MrBFlt re;
     MrBFlt im;
 };
-
 typedef struct complex complex;
 
 typedef struct