fixes while building

diff --git a/makefile b/makefile
index 42e71a0e42bb0341c3cff63a8c616d6572537f4b..c67f0ba6bd2d5a3baf675edef32fbd15679259fc 100644 (file)
--- a/makefile
+++ b/makefile
@@ -12,11 +12,10 @@
 USEMPI ?= no
 64BIT_VERSION ?= yes
 USEREADLINE ?= yes
-CYGWIN_BUILD ?= no
 USECOMPRESSION ?= no
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"10/16/2013\""
-VERSION = "\"1.32.1\""
+RELEASE_DATE = "\"2/12/2014\""
+VERSION = "\"1.33.0\""
 FORTAN_COMPILER = gfortran
 FORTRAN_FLAGS = 
 
@@ -50,10 +49,6 @@ else
        CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
 endif
 
-ifeq  ($(strip $(CYGWIN_BUILD)),yes)
-    CXXFLAGS += -mno-cygwin
-    LDFLAGS += -mno-cygwin 
-endif
 
 # if you do not want to use the readline library, set this to no.
 # make sure you have the library installed

diff --git a/pam.cpp b/pam.cpp
index 98b2113238f099dfb188a2235e87be0c76d230f4..d962a363f8330a063a1d63ac2129686164bc706f 100644 (file)
--- a/pam.cpp
+++ b/pam.cpp
@@ -125,10 +125,10 @@ int Pam::swapPhase() {
                             for (int j = 0; j < numSamples; j++) {
                                 if (m->control_pressed) { break; }
                                 if (dists[i][j] == Dp[j][0]) {
-                                    double small = 0.0;
-                                    if (Dp[j][1] > dists[h][j]) {   small = dists[h][j];    }
-                                    else                        {   small = Dp[j][1];       }
-                                    dz += (- Dp[j][0]+ small);
+                                    double smallValue; smallValue = 0.0;
+                                    if (Dp[j][1] > dists[h][j]) {   smallValue = dists[h][j];    }
+                                    else                        {   smallValue = Dp[j][1];       }
+                                    dz += (- Dp[j][0]+ smallValue);
                                 }else if (dists[h][j] < Dp[j][0]) {
                                     dz += (- Dp[j][0] + dists[h][j]);
                                 }