Merge pull request #25 from dwcaress/caress-tmp

Release 5.6.20181217

ChangeLog

@@ -15,6 +15,7 @@ MB-SYSTEM VERSION 5 RELEASE DATES:
 Here "*" denotes source distribution release made available for ftp download.
 Releases without an "*" are discrete revisions available from the source code
 archive at http://svn.ilab.ldeo.columbia.edu/listing.php?repname=MB-System.
+* Version 5.6.20181217   December 17, 2018
   Version 5.6.20181214   December 14, 2018
   Version 5.6.20181129   November 29, 2018
   Version 5.6.20181016   October 16, 2018
@@ -292,10 +293,17 @@ archive at http://svn.ilab.ldeo.columbia.edu/listing.php?repname=MB-System.
 -------------------------------------------------------------------------------
 MB-SYSTEM VERSION 5.6 RELEASE NOTES:
 -------------------------------------------------------------------------------
+
+-----> 5.6.20181217 (December 17, 2018)
+
+Memory management: Fixed memory leak associated with allocation and deallocation
+of edit save file (*.esf) data.
+
 -----> 5.6.20181214 (December 14, 2018)
 
 Format 121 (MBF_GSFGENMB): Changed GSFlib version to 3.08. MB-System also now
-builds and installs the program dump_gsf.
+builds and installs the program dump_gsf. Fixed several array overruns in the GSFlib
+source code distributed by Leidos.
 
 MBgrid: Added two new gridding algorithms, minimum weighted mean and maximum
 weighted mean. These are both implementations of Gaussian weighted mean in which

autom4te.cache/output.4

@@ -1,6 +1,6 @@
 @%:@! /bin/sh
 @%:@ Guess values for system-dependent variables and create Makefiles.
-@%:@ Generated by GNU Autoconf 2.69 for mbsystem 5.6.20181214.
+@%:@ Generated by GNU Autoconf 2.69 for mbsystem 5.6.20181217.
 @%:@
 @%:@ Report bugs to <http://listserver.mbari.org/sympa/arc/mbsystem>.
 @%:@ 
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='mbsystem'
 PACKAGE_TARNAME='mbsystem'
-PACKAGE_VERSION='5.6.20181214'
-PACKAGE_STRING='mbsystem 5.6.20181214'
+PACKAGE_VERSION='5.6.20181217'
+PACKAGE_STRING='mbsystem 5.6.20181217'
 PACKAGE_BUGREPORT='http://listserver.mbari.org/sympa/arc/mbsystem'
 PACKAGE_URL='http://www.mbari.org/data/mbsystem/'
 
@@ -1395,7 +1395,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures mbsystem 5.6.20181214 to adapt to many kinds of systems.
+\`configure' configures mbsystem 5.6.20181217 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1465,7 +1465,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of mbsystem 5.6.20181214:";;
+     short | recursive ) echo "Configuration of mbsystem 5.6.20181217:";;
    esac
   cat <<\_ACEOF
 
@@ -1612,7 +1612,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-mbsystem configure 5.6.20181214
+mbsystem configure 5.6.20181217
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2057,7 +2057,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by mbsystem $as_me 5.6.20181214, which was
+It was created by mbsystem $as_me 5.6.20181217, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2398,7 +2398,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
-$as_echo "@%:@define VERSION_DATE \"14 December 2018\"" >>confdefs.h
+$as_echo "@%:@define VERSION_DATE \"17 December 2018\"" >>confdefs.h
 
 
 ac_aux_dir=
@@ -3077,7 +3077,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='mbsystem'
- VERSION='5.6.20181214'
+ VERSION='5.6.20181217'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -16433,7 +16433,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by mbsystem $as_me 5.6.20181214, which was
+This file was extended by mbsystem $as_me 5.6.20181217, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -16500,7 +16500,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-mbsystem config.status 5.6.20181214
+mbsystem config.status 5.6.20181217
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for mbsystem 5.6.20181214.
+# Generated by GNU Autoconf 2.69 for mbsystem 5.6.20181217.
 #
 # Report bugs to <http://listserver.mbari.org/sympa/arc/mbsystem>.
 #
@@ -590,8 +590,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='mbsystem'
 PACKAGE_TARNAME='mbsystem'
-PACKAGE_VERSION='5.6.20181214'
-PACKAGE_STRING='mbsystem 5.6.20181214'
+PACKAGE_VERSION='5.6.20181217'
+PACKAGE_STRING='mbsystem 5.6.20181217'
 PACKAGE_BUGREPORT='http://listserver.mbari.org/sympa/arc/mbsystem'
 PACKAGE_URL='http://www.mbari.org/data/mbsystem/'
 
@@ -1395,7 +1395,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures mbsystem 5.6.20181214 to adapt to many kinds of systems.
+\`configure' configures mbsystem 5.6.20181217 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1465,7 +1465,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of mbsystem 5.6.20181214:";;
+     short | recursive ) echo "Configuration of mbsystem 5.6.20181217:";;
    esac
   cat <<\_ACEOF
 
@@ -1612,7 +1612,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-mbsystem configure 5.6.20181214
+mbsystem configure 5.6.20181217
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2057,7 +2057,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by mbsystem $as_me 5.6.20181214, which was
+It was created by mbsystem $as_me 5.6.20181217, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2398,7 +2398,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
-$as_echo "#define VERSION_DATE \"14 December 2018\"" >>confdefs.h
+$as_echo "#define VERSION_DATE \"17 December 2018\"" >>confdefs.h
 
 
 ac_aux_dir=
@@ -3077,7 +3077,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='mbsystem'
- VERSION='5.6.20181214'
+ VERSION='5.6.20181217'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -16433,7 +16433,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by mbsystem $as_me 5.6.20181214, which was
+This file was extended by mbsystem $as_me 5.6.20181217, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -16500,7 +16500,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-mbsystem config.status 5.6.20181214
+mbsystem config.status 5.6.20181217
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -19,11 +19,11 @@ define([AC_CACHE_LOAD], )
 define([AC_CACHE_SAVE], )
 
 dnl Initialize and set version and version date
-AC_INIT([mbsystem],[5.6.20181214],[http://listserver.mbari.org/sympa/arc/mbsystem],[mbsystem],[http://www.mbari.org/data/mbsystem/])
+AC_INIT([mbsystem],[5.6.20181217],[http://listserver.mbari.org/sympa/arc/mbsystem],[mbsystem],[http://www.mbari.org/data/mbsystem/])
 
 AC_CONFIG_MACRO_DIR(m4)
 AC_LANG(C)
-AC_DEFINE(VERSION_DATE, "14 December 2018", [Set VERSION_DATE define in mb_config.h])
+AC_DEFINE(VERSION_DATE, "17 December 2018", [Set VERSION_DATE define in mb_config.h])
 
 dnl Check system arch
 AC_CANONICAL_HOST

libtool

@@ -1,6 +1,6 @@
 #! /bin/sh
-# Generated automatically by config.status (mbsystem) 5.6.20181214
-# Libtool was configured on host Haxby.local:
+# Generated automatically by config.status (mbsystem) 5.6.20181217
+# Libtool was configured on host haxby.shore.mbari.org:
 # NOTE: Changes made to this file will be lost: look at ltmain.sh.
 
 # Provide generalized library-building support services.

src/mbedit/mbedit_prog.c

@@ -4029,7 +4029,7 @@ int mbedit_close_file() {
 
 	/* close the files */
 	status = mb_close(verbose, &imbio_ptr, &error);
-	if (esf.nedit > 0 || esf.esffp != NULL) {
+	if (esf.edit != NULL || esf.esffp != NULL) {
 		status = mb_esf_close(verbose, &esf, &error);
 	}
 

src/mbio/mb_config.h

@@ -83,7 +83,7 @@
 #define PACKAGE_NAME "mbsystem"
 
 /* Define to the full name and version of this package. */
-#define PACKAGE_STRING "mbsystem 5.6.20181214"
+#define PACKAGE_STRING "mbsystem 5.6.20181217"
 
 /* Define to the one symbol short name of this package. */
 #define PACKAGE_TARNAME "mbsystem"
@@ -92,16 +92,16 @@
 #define PACKAGE_URL "http://www.mbari.org/data/mbsystem/"
 
 /* Define to the version of this package. */
-#define PACKAGE_VERSION "5.6.20181214"
+#define PACKAGE_VERSION "5.6.20181217"
 
 /* Define to 1 if you have the ANSI C header files. */
 #define STDC_HEADERS 1
 
 /* Version number of package */
-#define VERSION "5.6.20181214"
+#define VERSION "5.6.20181217"
 
 /* Set VERSION_DATE define in mb_config.h */
-#define VERSION_DATE "14 December 2018"
+#define VERSION_DATE "17 December 2018"
 
 /* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most
    significant byte first (like Motorola and SPARC, unlike Intel). */

src/mbvelocitytool/mbvelocity_prog.c

@@ -2249,7 +2249,7 @@ int mbvt_open_swath_file(char *file, int form, int *numload) {
 	status = mb_close(verbose, &mbio_ptr, &error);
 
 	/* Close ESF file if avialable */
-	if (esf.nedit > 0)
+	if (esf.edit != NULL || esf.esffp != NULL)
 		mb_esf_close(verbose, &esf, &error);
 
 	/* define success */

src/utilities/mbbackangle.c

@@ -1295,7 +1295,7 @@ by MBprocess.";
 		/* close the swath sonar file */
 		status = mb_close(verbose, &mbio_ptr, &error);
 		/* Close ESF file if avialable and open */
-		if (esf.nedit > 0)
+		if (esf.edit != NULL || esf.esffp != NULL)
 			mb_esf_close(verbose, &esf, &error);
 
 		if (dump == MB_NO && amplitude_on == MB_YES)

src/utilities/mbprocess.c

@@ -352,7 +352,7 @@ and mbedit edit save files.\n";
 	int neditduplicate;
 	int neditnotused;
 	int neditused;
-	
+
 	/* output reverse edit save file control variables */
 	mb_path resf_file;
 	FILE *resf_fp = NULL;
@@ -411,7 +411,7 @@ and mbedit edit save files.\n";
 
 	/* topography parameters */
 	struct mbprocess_grid_struct grid;
-	
+
 	/* output fbt and fnv files */
 	FILE *fnv_fp, *fbt_fp;
 	mb_path fnv_file, fbt_file;
@@ -3144,7 +3144,7 @@ and mbedit edit save files.\n";
 			/* reset error */
 			error = MB_ERROR_NO_ERROR;
 			status = MB_SUCCESS;
-			
+
 			/* open reverse edit save file (*.resf) */
 			sprintf(resf_file, "%s.resf", process.mbp_ifile);
 			if ((resf_fp = fopen(resf_file, "w")) == NULL) {
@@ -4255,7 +4255,7 @@ and mbedit edit save files.\n";
 						status = MB_FAILURE;
 					}
 				}
-				
+
 				/* save the orignal beamflag states */
 				if (error == MB_ERROR_NO_ERROR && kind == MB_DATA_DATA) {
 					for (i = 0; i < nbath; i++) {
@@ -5599,7 +5599,7 @@ and mbedit edit save files.\n";
 					                   namp, nss, beamflag, bath, amp, bathacrosstrack, bathalongtrack, ss, ssacrosstrack,
 					                   ssalongtrack, comment, &error);
 				}
-				
+
 				/*--------------------------------------------
 				  output any changed beamflags to the reverse
 				  edit save file (saving the change required
@@ -5714,7 +5714,7 @@ and mbedit edit save files.\n";
 			/* unlock the raw swath file */
 			if (uselockfiles == MB_YES)
 				lock_status = mb_pr_unlockswathfile(verbose, process.mbp_ifile, MBP_LOCK_PROCESS, program_name, &lock_error);
-				
+
 			/* close the *.resf file */
 			if (resf_fp != NULL) {
 				fclose(resf_fp);
@@ -5799,7 +5799,7 @@ and mbedit edit save files.\n";
 			}
 
 			/* deallocate arrays for beam edits */
-			if (esf.nedit > 0) {
+			if (process.mbp_edit_mode == MBP_EDIT_ON) {
 				mb_esf_close(verbose, &esf, &error);
 			}