merging 1.2 into newseq

git-svn-id: svn://scit.us/dawg/branches/newseq@373 7e5b8c5c-87e2-0310-a459-8d91125b37d5
reedacartwright · Sep 4, 2009 · 2eb599c · 2eb599c
1 parent 72e2da9
commit 2eb599c
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Showing 6 changed files with 21 additions and 18 deletions.
diff --git a/Modules/CMakeUserUseBison.cmake b/Modules/CMakeUserUseBison.cmake
@@ -50,23 +50,24 @@ IF(BISON_EXECUTABLE)
    SET(OUTFILE "${CMAKE_CURRENT_BINARY_DIR}${PATH_OPT}/${HEAD}.tab${EXT}")
    IF(BISON_GENERATE_DEFINES)
      SET(HEADER "${CMAKE_CURRENT_BINARY_DIR}${PATH_OPT}/${HEAD}.tab${HEXT}")
-     ADD_CUSTOM_COMMAND(
-       OUTPUT "${OUTFILE}" "${HEADER}"
-       COMMAND "${BISON_EXECUTABLE}"
-       ARGS "--name-prefix=${PREFIX}"
-       "--defines"
-       "--output-file=${OUTFILE}"
-       "${CMAKE_CURRENT_SOURCE_DIR}/${FILENAME}"
+	 IF(UNIX OR NOT WIN32)
+		SET(BISON_TEST_MV && \( \( test -f "${OUTFILE}.h"
+		  && mv "${OUTFILE}.h" "${HEADER}" \) || true \)
+		  && test -f "${HEADER}"
+		)
+	 ENDIF(UNIX OR NOT WIN32)
+
+     ADD_CUSTOM_COMMAND( OUTPUT "${OUTFILE}" "${HEADER}"
+       COMMAND "${BISON_EXECUTABLE}" -p "${PREFIX}" -o "${OUTFILE}" -d
+          "${CMAKE_CURRENT_SOURCE_DIR}/${FILENAME}"
+	   ${BISON_TEST_MV}
        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/${FILENAME}")
      SET_SOURCE_FILES_PROPERTIES("${OUTFILE}" "${HEADER}" PROPERTIES GENERATED TRUE)
      SET_SOURCE_FILES_PROPERTIES("${HEADER}" PROPERTIES HEADER_FILE_ONLY TRUE)
    ELSE(BISON_GENERATE_DEFINES)
-     ADD_CUSTOM_COMMAND(
-       OUTPUT "${OUTFILE}"
-       COMMAND "${BISON_EXECUTABLE}"
-       ARGS "--name-prefix=${PREFIX}"
-       "--output-file=${OUTFILE}"
-       "${CMAKE_CURRENT_SOURCE_DIR}/${FILENAME}"
+     ADD_CUSTOM_COMMAND( OUTPUT "${OUTFILE}"
+       COMMAND "${BISON_EXECUTABLE}" -p "${PREFIX}" -o "${OUTFILE}"
+           "${CMAKE_CURRENT_SOURCE_DIR}/${FILENAME}"
        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/${FILENAME}")
      SET_SOURCE_FILES_PROPERTIES("${OUTFILE}" PROPERTIES GENERATED TRUE)
    ENDIF(BISON_GENERATE_DEFINES)

diff --git a/lambda.pl b/lambda.pl
@@ -462,8 +462,9 @@ sub rsq
 		$m += $obs[$i];
 		$m2 += $obs[$i]*$obs[$i];
 	}
-	return 1.0 - $SSe/($m2-$m*$m/@obs);
-
+	my $SSt = $m2-$m*$m/@obs;
+	return "NA" if($SSt == 0);
+	return 1.0 - $SSe/$SSt;
 }
 
 

diff --git a/releng/build-rel-osx.sh b/releng/build-rel-osx.sh
@@ -2,10 +2,9 @@
 
 PROJ=dawg
 PROJ_DISTS=dawg-1*
-
 MAKE=make
 CMAKE=cmake
-REPOS=`svn info | grep URL: | perl -pe "s!^URL: (.+)/releng$!$1!"`
+REPOS=`svn info | grep URL: | perl -pe 's!^URL: (.+)/releng$!$1!'`
 
 echo 
 echo Building distributions for $REPOS ...

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -56,6 +56,7 @@ CHECK_INCLUDE_FILE(process.h HAVE_PROCESS_H)
 CHECK_INCLUDE_FILE(io.h HAVE_IO_H)
 CHECK_INCLUDE_FILE(getopt.h  HAVE_GETOPT_H)
 CHECK_INCLUDE_FILE(stdint.h  HAVE_STDINT_H)
+CHECK_INCLUDE_FILE(sys/types.h HAVE_SYS_TYPES_H)
 
 CHECK_FUNCTION_EXISTS( getpid   HAVE_GETPID)
 CHECK_FUNCTION_EXISTS(_getpid   HAVE__GETPID)

diff --git a/src/config.h.cmake b/src/config.h.cmake
@@ -7,7 +7,7 @@
 #cmakedefine HAVE_IO_H 1
 #cmakedefine HAVE_GETOPT_H  1
 #cmakedefine HAVE_STDINT_H  1
-
+#cmakedefine HAVE_SYS_TYPES_H 1
 
 #cmakedefine HAVE_GETPID    1
 #cmakedefine HAVE__GETPID   1

diff --git a/src/dawg.h b/src/dawg.h
@@ -37,6 +37,7 @@
 #include <cmath>
 #include <cassert>
 #include <cstdarg>
+#include <cstring>
 
 #include <vector>
 #include <string>