CMakeLists.txt

@@ -420,6 +420,31 @@ if(WITH_EXPAT)
         message(FATAL_ERROR
 "The include directory specified for Expat appears to be invalid.
 It should contain the file expat.h, but it does not.")
+    else()
+        if (LIBEXPAT_INCLUDE_DIR AND EXISTS "${LIBEXPAT_INCLUDE_DIR}/expat.h")
+            file(STRINGS "${LIBEXPAT_INCLUDE_DIR}/expat.h" expat_version_str
+                 REGEX "^#[\t ]*define[\t ]+XML_(MAJOR|MINOR|MICRO)_VERSION[\t ]+[0-9]+$")
+
+            unset(EXPAT_VERSION_STRING)
+            foreach(VPART MAJOR MINOR MICRO)
+                foreach(VLINE ${expat_version_str})
+                    if(VLINE MATCHES "^#[\t ]*define[\t ]+XML_${VPART}_VERSION[\t ]+([0-9]+)$")
+                        set(EXPAT_VERSION_PART "${CMAKE_MATCH_1}")
+                        if(EXPAT_VERSION_STRING)
+                            set(EXPAT_VERSION_STRING "${EXPAT_VERSION_STRING}.${EXPAT_VERSION_PART}")
+                        else()
+                            set(EXPAT_VERSION_STRING "${EXPAT_VERSION_PART}")
+                        endif()
+                    endif()
+                endforeach()
+            endforeach()
+
+            if (EXPAT_VERSION_STRING VERSION_LESS 1.95.9)
+                     message(FATAL_ERROR
+"Expat version ${EXPAT_VERSION_STRING} is not compatible with libSBML.
+Please use a version newer than 1.95.8 or an alternate XML parser.")
+            endif()
+        endif()
     endif()
 endif(WITH_EXPAT)
 
@@ -494,6 +519,39 @@ if(WITH_XERCES)
         DOC "The directory containing the Xerces include files."
               )
 
+    if (EXISTS "${XERCES_INCLUDE_DIR}/xercesc/util/XercesVersion.hpp")
+        function(_myXercesC_GET_VERSION  version_hdr)
+            file(STRINGS ${version_hdr} _contents REGEX "^[ \t]*#define XERCES_VERSION_.*")
+            if(_contents)
+                string(REGEX REPLACE ".*#define XERCES_VERSION_MAJOR[ \t]+([0-9]+).*" "\\1" XercesC_MAJOR "${_contents}")
+                string(REGEX REPLACE ".*#define XERCES_VERSION_MINOR[ \t]+([0-9]+).*" "\\1" XercesC_MINOR "${_contents}")
+                string(REGEX REPLACE ".*#define XERCES_VERSION_REVISION[ \t]+([0-9]+).*" "\\1" XercesC_PATCH "${_contents}")
+
+                if(NOT XercesC_MAJOR MATCHES "^[0-9]+$")
+                    message(FATAL_ERROR "Version parsing failed for XERCES_VERSION_MAJOR!")
+                endif()
+                if(NOT XercesC_MINOR MATCHES "^[0-9]+$")
+                    message(FATAL_ERROR "Version parsing failed for XERCES_VERSION_MINOR!")
+                endif()
+                if(NOT XercesC_PATCH MATCHES "^[0-9]+$")
+                    message(FATAL_ERROR "Version parsing failed for XERCES_VERSION_REVISION!")
+                endif()
+
+                set(XercesC_VERSION "${XercesC_MAJOR}.${XercesC_MINOR}.${XercesC_PATCH}" PARENT_SCOPE)
+            else()
+                message(FATAL_ERROR "Include file ${version_hdr} does not exist or does not contain expected version information")
+            endif()
+        endfunction()
+
+        _myXercesC_GET_VERSION("${XERCES_INCLUDE_DIR}/xercesc/util/XercesVersion.hpp")
+        if (XercesC_VERSION VERSION_EQUAL 2.6.0)
+         message(FATAL_ERROR
+"Xerces version ${XercesC_VERSION} contains known bugs
+and is not compatible with libSBML. Please use a newer version of
+Xerces or an alternate XML parser.")
+        endif()
+    endif ()
+
     set(LIBSBML_XML_LIBRARY "xerces-c")
     set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR})
     set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY})
@@ -507,7 +565,6 @@ it does not.")
 
 endif(WITH_XERCES)
 
-
 ###############################################################################
 #
 # Locate bz2
@@ -953,7 +1010,7 @@ else(UNIX)
             NAMES vld.h
             PATHS ${LIBSBML_DEPENDENCY_DIR}/include
             "$ENV{PROGRAMFILES}/Visual Leak Detector/include"
-          "$ENV{PROGRAMFILES(X86)}/Visual Leak Detector/include"
+            "$ENV{ProgramW6432}/Visual Leak Detector/include"
             DOC "Directory containing VLD files."
           )
           if (NOT VLD_INCLUDE_DIR)

Makefile.in

@@ -259,6 +259,7 @@ examples =                                                          \
   examples/perl/printUnits.pl                                       \
   examples/perl/promoteParameters.pl                                \
   examples/perl/readSBML.pl                                         \
+  examples/perl/renameSId.pl                                        \
   examples/perl/translateMath.pl                                    \
   examples/perl/unsetAnnotation.pl                                  \
   examples/perl/unsetNotes.pl                                       \
@@ -286,6 +287,7 @@ examples =                                                          \
   examples/python/printUnits.py                                     \
   examples/python/promoteParameters.py                              \
   examples/python/readSBML.py                                       \
+  examples/python/stringInput.py                                    \
   examples/python/setIdFromNames.py                                 \
   examples/python/translateMath.py                                  \
   examples/python/unsetAnnotation.py                                \

NEWS.txt

            libSBML NEWS -- History of user-visible changes
 
 
+====================================================================
+5.16.0 (2017-12-07)
+====================================================================
+
+
+
+STABLE RELEASE
+
+* Note
+
+  The L3 Render Package has been approved by the SBML Editors, but
+  approval came too late in the libSBML release cycle to include it
+  in this stable release of libSBML.
+
+  There are now two implementations of support for SBML Level 3
+  Version 2 Core.  The libSBML code for L3V2 can now be considered
+  stable and will only change for bug fixes.
+
+* New features
+
+  - The MATLAB interface now supports both the 'qual' and 'groups' 
+    packages, in addition to 'fbc'. 
+
+  - Unit checking has been expanded to include checking the <math>
+    of <trigger>, <constraint> and <stoichiometryMath> to at least
+    allow detection of values with undeclared units.
+
+  - Writing out an XMLNode that represented XHTML with multiple
+    nested text elements could distrupt indentation (see bug fixes).
+    A new function XMLNode::writeToStream(XMLOutputStream&) checks
+    the indentation is correctly recovered after writing out the
+    XMLNode.
+	
+  - 'comp' package-specific updates:
+
+    - There has been some improvements made to the reporting of line
+      numbers for errors and warnings.
+
+* Bug fixes
+
+  - SF Tracker #450: Code validating the shadowing of localParameter
+    was checking both 'id' and 'species' attributes. This rule should
+    only check the species attribute.
+
+  - SBML validation failed to distinguish between LocalParameters and
+    Parameters in L3V1 when reporting errors. This is fixed.
+
+  - libSBML had incorrectly reported that the 'fast' attribute was a
+    required attribute of L3V2 <reaction> elements. This is fixed.
+
+  - The libSBML C API does not work with default arguments. There were
+    previously a few stray ones left in the API code. These have been
+    removed.
+
+  - The SBMLTransforms::evaluateASTNode function previously failed to
+    check that model values had been evaluated prior to trying to
+    evaluate an ASTNode. The relevant function now checks whether the
+    map of values is present and populates it, if necessary.
+
+  - Code that checked the syntax for attributes of type ID and IDREF
+    did not always use the appropriate function. These cases have been
+    fixed.
+
+  - The use of an invalid syntax as the sbml:units attribute on a math
+    <cn> element was not being detected. This has been fixed. Thanks
+    to Nicolas Rodriguez for the report.
+
+  - The SBMLTransforms::evaluateASTNode function missed the fact that
+    in SBML Level 2, stoichiometry defaulted to '1'. This has been
+    corrected.
+
+  - The use of certain combinations of text elements in a <notes> element
+    could derail the entire indentation of the document. This has been
+    reported by several people. Hopefully this time we have fixed the
+    situation for all cases where it may occur. 
+
+  - The interactive help text stored with the functions and classes in
+    the Python bindings had many formatting problems and outright
+    omissions due to bugs in our "rewrite_pydoc.py" code. Many of
+    these problems should be fixed now.
+
+  - 'fbc' package-specific bug fixes:
+
+    - Validation incorrectly reported an empty <listOfFluxObjectives>
+      even when a model was being created and did in fact have a
+      <fluxObjective> element. This has been fixed. Thanks to Arthur
+      Goldberg for reporting it.
+
+    - An empty <geneProductAssociation> caused the reading of model
+      files to crash libSBML. This no longer happens.
+
+  - 'layout' package-specific bug fixes:
+
+    - Conversion between Level 2 annotations using both layout and render
+      and Level 3 packages has been corrected.
+  
+  - 'qual' package-specific bug fixes:
+
+     - Functions to get math on a <functionTerm> element were missing
+       from the C API. They have been added.
+
+* Configuration/build system changes
+
+  - SourceForge Tracker item #447: Configuration no longer defines
+    HAVE_IEEEFP_H when using MSVC compilers as it is not needed 
+    and not always present. Thanks to Alan Garny for spotting this.
+
+  - SourceForge Tracker item #443 & separate unreported problems:
+    Build failures with Java 9 should be fixed now.  Thanks to Chris
+    West for reporting the issue related to building the docs.
+
+* Miscellaneous
+
+  - SWIG only supports Javascript node 6x. Thus we cannot currently
+    support later versions of node.
+
+  - Documentation for the C API has been extensively improved.
+
+  - Support has been added for Python 2 unicode input.
+
+  - Currently we supply lib files built with MSVC2010 as part of the 
+    windows installers. These will be removed from future releases. 
+    Please let us know if this is an issue for you.
+
+
+EXPERIMENTAL RELEASE
+
+* New features
+
+  - 'render' package-specific updates:
+
+    - At the request of the SBMLEditors the attribute 'name' has been
+      added to render elements.
+
+ * Bug fixes
+ 
+  - 'render' package-specific bug fixes:
+
+    - Conversion between Level 2 annotations using both layout and
+      render and Level 3 packages has been corrected.
+
+  - 'spatial' package-specific bug fixes:
+
+    - There was a mismatch in the SetOperation enumeration in the
+      specification.  This has been agreed as 'union', 'intersection'
+      and 'difference' and libSBML code has changed to reflect this.
+
+    - Corrected the output of a <csGeometry> element to correctly use
+      an upper case G.
+      
+
+
 ====================================================================
 5.15.2 (2017-07-27)
 ====================================================================

README.txt

@@ -288,16 +288,12 @@ experienced the issue and offer a workaround more quickly than the
 libSBML developers can respond.
 
 
-5. MAILING LISTS
+5. FORUMS AND MAILING LISTS
 ======================================================================
 
-There are two kinds of mailing lists available: normal discussion
-lists for humans, and a SVN change notification list.
-
-Discussion lists
-----------------
-
-All discussion lists, their web interfaces and their RSS feeds are at
+There are different forums/mailing lists available for SBML. Most are
+hosted by Google Groups; a few legacy lists are still operated as
+SourceForge mailing lists. You can find a list of all of them here:
 
                        http://sbml.org/Forums/
 
@@ -316,16 +312,6 @@ of libsbml-development will enable you to keep in touch with the
 latest developments in libSBML as well as to ask questions and share
 your experiences with fellow developers and users of libSBML.
 
-SVN notification
-----------------
-
-If you are obtaining your libSBML files from SVN, you may wish to
-subscribe to the mailing list sbml-svn, to be apprised of changes to
-the SVN repository as soon as they are committed.  You can join the
-list by visiting the following URL:
-
-  https://lists.sourceforge.net/lists/listinfo/sbml-svn
-
 
 6. LICENSING AND DISTRIBUTION
 ======================================================================

VERSION.txt

-5.15.2
+5.16.0

aclocal.m4

-# generated automatically by aclocal 1.15 -*- Autoconf -*-
+# generated automatically by aclocal 1.15.1 -*- Autoconf -*-
 
-# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Copyright (C) 1996-2017 Free Software Foundation, Inc.
 
 # This file is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,

config/java.m4

@@ -62,9 +62,9 @@ AC_DEFUN([CONFIG_PROG_JAVA],
 
       with_java=`echo $with_java | sed -e 's,\(.*\)/$,\1,g'`
 
-      AC_PATH_PROG([JAVA], [java], [no], [$with_java/bin])
-      AC_PATH_PROG([JAVAC], [javac], [no], [$with_java/bin])
-      AC_PATH_PROG([JAR], [jar], [no], [$with_java/bin])
+      AC_PATH_PROG([JAVA], [java], [no], [$with_java/bin $with_java])
+      AC_PATH_PROG([JAVAC], [javac], [no], [$with_java/bin $with_java])
+      AC_PATH_PROG([JAR], [jar], [no], [$with_java/bin $with_java])
     else
       dnl No prefix directory path supplied for --with-java.  Use defaults.
 
@@ -95,26 +95,24 @@ AC_DEFUN([CONFIG_PROG_JAVA],
 
       version=`"$JAVA" -version 2>&1 | sed -e 's/openjdk/java/' | sed -e 's/-internal//'| sed -e 's/\(.*\)$/\1/;q'`
 
-      jx=`echo $version | sed -e 's/java version \"\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1/'`
+      jx=`echo $version | sed -e 's/java version \"\([0-9]\).*/\1/'`
       jy=`echo $version | sed -e 's/java version \"\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\2/'`
       jz=`echo $version | sed -e 's/java version \"\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\3/'`
 
       changequote([, ])
 
-      if test $jx -gt $rx \
-         || (test $jx -eq $rx -a $jy -gt $ry) \
-         || (test $jx -eq $rx -a $jy -eq $ry -a $jz -ge $rz); then
-        AC_MSG_RESULT(yes (found $jx.$jy.$jz))
+      if test $jx -gt 1; then
+        dnl Java switched versioning from 1.9 to 9.
+        JAVA_VERSION=$jx
+        AC_MSG_RESULT(yes (found version $version))
+      elif test $jy -gt $ry; then
+        dnl Old-style Java version numbers are 1.y.z, where y is important.
+        JAVA_VERSION=$jy
+        AC_MSG_RESULT(yes (found version $version))
       else
         AC_MSG_RESULT(no)
-        AC_MSG_ERROR([Need Java version $1, but only found version $jx.$jy.$jz.])
+        AC_MSG_ERROR([Need Java version $1, but only found version $version])
       fi
-
-      dnl Retain these for use below.
-
-      JAVA_VER_MINOR=$jy
-      JAVA_VER_SUBMINOR=$jz
-
     ])
 
     dnl Look for the path to jni.h.
@@ -170,7 +168,14 @@ AC_DEFUN([CONFIG_PROG_JAVA],
     case "$host" in
       *darwin*)
         framework="/System/Library/Frameworks/JavaVM.framework"
-        case $JAVA_VER_MINOR in
+        case $JAVA_VERSION in
+          9)
+            if test -e "$framework/Versions/Current/Headers"; then
+              headers="$framework/Versions/Current/Headers"
+            elif test -e "$framework/Versions/CurrentJDK/Headers"; then
+              headers="$framework/Versions/CurrentJDK/Headers"
+            fi
+            ;;
           8)
             if test -e "$framework/Versions/Current/Headers"; then
               headers="$framework/Versions/Current/Headers"
@@ -212,34 +217,27 @@ AC_DEFUN([CONFIG_PROG_JAVA],
         esac
 
         if ! test -e "$headers/jni.h"; then
-          if test $macosx_minor_vers -ge 9; then
-            AC_MSG_ERROR([
-Cannot find Java include files.  
-Note that Mac OS X 10.9 (Mavericks) does not provide a JDK by default.
-You may need to install Apple's "Java for OS X Developer Package"
-distribution, which you can find by visiting http://developer.apple.com
-and searching for "java", then selecting the most recent distribution.
-At the time of this writing, the full name was "Java for OS X 2013-005
-Developer Package".  As an alternative, you can try to use Oracle's
-distribution of Java for Mac OS X.
-])
-          else
           AC_MSG_ERROR([
 Cannot find Java include files. Your environment may lack a Java
 development kit installation.
 ])
         fi
-        fi
 
         JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I\"$headers\""
 
         parent=`dirname "$headers"`
-        if test -e "$parent/Classes/classes.jar"; then
+        if test $JAVA_VERSION -ge 9; then
+	  JAVADOC_JAR=
+        elif test -e "$parent/Classes/classes.jar"; then
           JAVADOC_JAR="$parent/Classes/classes.jar"
         elif test -e "$parent/Classes/tools.jar"; then
           JAVADOC_JAR="$parent/Classes/tools.jar"
         elif test -e "${parent}JDK/Classes/classes.jar"; then
           JAVADOC_JAR="${parent}JDK/Classes/classes.jar"
+        elif test -e "/usr/libexec/java_home"; then
+          JAVADOC_JAR=`/usr/libexec/java_home`/lib/tools.jar
+        else
+          JAVADOC_JAR="$parent/lib/tools.jar"
         fi
       ;;
 
@@ -285,8 +283,6 @@ development kit installation.
           linux*)   JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I\"$parent/include/linux\"";;
           solaris*) JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I\"$parent/include/solaris\"";;
         esac
-
-        JAVADOC_JAR="$parent/lib/tools.jar"
       ;;
     esac
 
@@ -629,6 +625,7 @@ the options for configure to bypass this architecture check.
 
     AC_SUBST(JAVA_CPPFLAGS)
     AC_SUBST(JAVA_LDFLAGS)
+    AC_SUBST(JAVA_VERSION)
     AC_SUBST(JNIEXT)
     AC_SUBST(JNIBASENAME)
     AC_SUBST(JAVADOC_JAR)

config/makefile-common-vars.mk.in

@@ -126,6 +126,7 @@ RUBY_LDFLAGS      = @RUBY_LDFLAGS@
 RUBY_LIBS         = @RUBY_LIBS@
 
 USE_JAVA          = @USE_JAVA@
+JAVA_VERSION      = @JAVA_VERSION@
 JAVA              = @JAVA@
 JAVAC             = @JAVAC@
 JAR               = @JAR@

configure

 #! /bin/sh
-# From configure.ac Revision: 24150 .
+# From configure.ac Revision: 24507 .
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for libSBML 5.15.2.
+# Generated by GNU Autoconf 2.69 for libSBML 5.16.0.
 #
 # Report bugs to <libsbml-team@googlegroups.com>.
 #
@@ -735,8 +735,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='libSBML'
 PACKAGE_TARNAME='libsbml'
-PACKAGE_VERSION='5.15.2'
-PACKAGE_STRING='libSBML 5.15.2'
+PACKAGE_VERSION='5.16.0'
+PACKAGE_STRING='libSBML 5.16.0'
 PACKAGE_BUGREPORT='libsbml-team@googlegroups.com'
 PACKAGE_URL='http://sbml.org/Software/libSBML'
@@ -870,6 +870,7 @@ MATLAB
 JAVADOC_JAR
 JNIBASENAME
 JNIEXT
+JAVA_VERSION
 JAVA_LDFLAGS
 JAVA_CPPFLAGS
 USE_JAVA
@@ -1609,7 +1610,7 @@ 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 libSBML 5.15.2 to adapt to many kinds of systems.
+\`configure' configures libSBML 5.16.0 to adapt to many kinds of systems.
 Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1674,7 +1675,7 @@ fi
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of libSBML 5.15.2:";;
+     short | recursive ) echo "Configuration of libSBML 5.16.0:";;
    esac
   cat <<\_ACEOF
@@ -1828,7 +1829,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-libSBML configure 5.15.2
+libSBML configure 5.16.0
 generated by GNU Autoconf 2.69
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2547,7 +2548,7 @@ 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 libSBML $as_me 5.15.2, which was
+It was created by libSBML $as_me 5.16.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   $ $0 $@
@@ -2937,7 +2938,7 @@ ac_config_headers="$ac_config_headers src/sbml/common/libsbml-package.h"
 ac_config_headers="$ac_config_headers src/sbml/common/libsbml-namespace.h"
-LIBSBML_VERSION_NUMERIC=51502
+LIBSBML_VERSION_NUMERIC=51600
@@ -2945,11 +2946,11 @@ LIBSBML_MAJOR_VERSION=5
-LIBSBML_MINOR_VERSION=15
-LIBSBML_REVISION_VERSION=2
+LIBSBML_MINOR_VERSION=16
+LIBSBML_REVISION_VERSION=0
@@ -5909,7 +5910,7 @@ else
   ;;
   *)
   as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $with_java/bin
+for as_dir in $with_java/bin $with_java
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
@@ -5950,7 +5951,7 @@ else
   ;;
   *)
   as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $with_java/bin
+for as_dir in $with_java/bin $with_java
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
@@ -5991,7 +5992,7 @@ else
   ;;
   *)
   as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $with_java/bin
+for as_dir in $with_java/bin $with_java
 do
   IFS=$as_save_IFS
   test -z "$as_dir" && as_dir=.
@@ -6164,29 +6165,27 @@ $as_echo_n "checking $JAVA version >= 1.5.0... " >&6; }
       version=`"$JAVA" -version 2>&1 | sed -e 's/openjdk/java/' | sed -e 's/-internal//'| sed -e 's/\(.*\)$/\1/;q'`
-      jx=`echo $version | sed -e 's/java version \"\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\1/'`
+      jx=`echo $version | sed -e 's/java version \"\([0-9]\).*/\1/'`
       jy=`echo $version | sed -e 's/java version \"\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\2/'`
       jz=`echo $version | sed -e 's/java version \"\([0-9]*\)\.\([0-9]*\)\.\([0-9]*\).*/\3/'`
-      if test $jx -gt $rx \
-         || (test $jx -eq $rx -a $jy -gt $ry) \
-         || (test $jx -eq $rx -a $jy -eq $ry -a $jz -ge $rz); then
-        { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes (found $jx.$jy.$jz)" >&5
-$as_echo "yes (found $jx.$jy.$jz)" >&6; }
+      if test $jx -gt 1; then
+                JAVA_VERSION=$jx
+        { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes (found version $version)" >&5
+$as_echo "yes (found version $version)" >&6; }
+      elif test $jy -gt $ry; then
+                JAVA_VERSION=$jy
+        { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes (found version $version)" >&5
+$as_echo "yes (found version $version)" >&6; }
       else
         { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
 $as_echo "no" >&6; }
-        as_fn_error $? "Need Java version 1.5.0, but only found version $jx.$jy.$jz." "$LINENO" 5
+        as_fn_error $? "Need Java version 1.5.0, but only found version $version" "$LINENO" 5
       fi
-      JAVA_VER_MINOR=$jy
-      JAVA_VER_SUBMINOR=$jz
-
-
-
@@ -6217,7 +6216,14 @@ $as_echo "no" >&6; }
     case "$host" in
       *darwin*)
         framework="/System/Library/Frameworks/JavaVM.framework"
-        case $JAVA_VER_MINOR in
+        case $JAVA_VERSION in
+          9)
+            if test -e "$framework/Versions/Current/Headers"; then
+              headers="$framework/Versions/Current/Headers"
+            elif test -e "$framework/Versions/CurrentJDK/Headers"; then
+              headers="$framework/Versions/CurrentJDK/Headers"
+            fi
+            ;;
           8)
             if test -e "$framework/Versions/Current/Headers"; then
               headers="$framework/Versions/Current/Headers"
@@ -6259,34 +6265,27 @@ $as_echo "no" >&6; }
         esac
         if ! test -e "$headers/jni.h"; then
-          if test $macosx_minor_vers -ge 9; then
-            as_fn_error $? "
-Cannot find Java include files.
-Note that Mac OS X 10.9 (Mavericks) does not provide a JDK by default.
-You may need to install Apple's \"Java for OS X Developer Package\"
-distribution, which you can find by visiting http://developer.apple.com
-and searching for \"java\", then selecting the most recent distribution.
-At the time of this writing, the full name was \"Java for OS X 2013-005
-Developer Package\".  As an alternative, you can try to use Oracle's
-distribution of Java for Mac OS X.
-" "$LINENO" 5
-          else
           as_fn_error $? "
 Cannot find Java include files. Your environment may lack a Java
 development kit installation.
 " "$LINENO" 5
         fi
-        fi
         JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I\"$headers\""
         parent=`dirname "$headers"`
-        if test -e "$parent/Classes/classes.jar"; then
+        if test $JAVA_VERSION -ge 9; then
+	  JAVADOC_JAR=
+        elif test -e "$parent/Classes/classes.jar"; then
           JAVADOC_JAR="$parent/Classes/classes.jar"
         elif test -e "$parent/Classes/tools.jar"; then
           JAVADOC_JAR="$parent/Classes/tools.jar"
         elif test -e "${parent}JDK/Classes/classes.jar"; then
           JAVADOC_JAR="${parent}JDK/Classes/classes.jar"
+        elif test -e "/usr/libexec/java_home"; then
+          JAVADOC_JAR=`/usr/libexec/java_home`/lib/tools.jar
+        else
+          JAVADOC_JAR="$parent/lib/tools.jar"
         fi
       ;;
@@ -6327,8 +6326,6 @@ development kit installation.
           linux*)   JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I\"$parent/include/linux\"";;
           solaris*) JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I\"$parent/include/solaris\"";;
         esac
-
-        JAVADOC_JAR="$parent/lib/tools.jar"
       ;;
     esac
@@ -6766,6 +6763,7 @@ $as_echo "#define USE_JAVA 1" >>confdefs.h
+
   fi
@@ -9199,12 +9197,12 @@ fi
     fi
-    DOXYGEN_MIN_VERSION=1.7.0
+    DOXYGEN_MIN_VERSION=1.8.8
     DOXYGEN_MAX_VERSION=1.8.11
-      { $as_echo "$as_me:${as_lineno-$LINENO}: checking $DOXYGEN version >= 1.7.0" >&5
-$as_echo_n "checking $DOXYGEN version >= 1.7.0... " >&6; }
+      { $as_echo "$as_me:${as_lineno-$LINENO}: checking $DOXYGEN version >= 1.8.8" >&5
+$as_echo_n "checking $DOXYGEN version >= 1.8.8... " >&6; }
       version=`"$DOXYGEN" --version | tr -d '\015'`
@@ -10015,7 +10013,7 @@ ia64-*-hpux*)
   ;;
 *-*-irix6*)
   # Find out which ABI we are using.
-  echo '#line 10018 "configure"' > conftest.$ac_ext
+  echo '#line 10016 "configure"' > conftest.$ac_ext
   if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
@@ -12233,11 +12231,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:12236: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:12234: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:12240: \$? = $ac_status" >&5
+   echo "$as_me:12238: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -12523,11 +12521,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:12526: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:12524: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:12530: \$? = $ac_status" >&5
+   echo "$as_me:12528: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -12627,11 +12625,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:12630: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:12628: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:12634: \$? = $ac_status" >&5
+   echo "$as_me:12632: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -14652,7 +14650,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 14655 "configure"
+#line 14653 "configure"
 #include "confdefs.h"
 #if HAVE_DLFCN_H
@@ -14752,7 +14750,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 14755 "configure"
+#line 14753 "configure"
 #include "confdefs.h"
 #if HAVE_DLFCN_H
@@ -17097,11 +17095,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:17100: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:17098: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:17104: \$? = $ac_status" >&5
+   echo "$as_me:17102: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -17201,11 +17199,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:17204: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:17202: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:17208: \$? = $ac_status" >&5
+   echo "$as_me:17206: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -18784,11 +18782,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:18787: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:18785: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:18791: \$? = $ac_status" >&5
+   echo "$as_me:18789: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -18888,11 +18886,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:18891: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:18889: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:18895: \$? = $ac_status" >&5
+   echo "$as_me:18893: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -21058,11 +21056,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:21061: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:21059: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:21065: \$? = $ac_status" >&5
+   echo "$as_me:21063: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -21348,11 +21346,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:21351: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:21349: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:21355: \$? = $ac_status" >&5
+   echo "$as_me:21353: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings other than the usual output.
@@ -21452,11 +21450,11 @@ else
    -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:21455: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:21453: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:21459: \$? = $ac_status" >&5
+   echo "$as_me:21457: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -27655,7 +27653,7 @@ 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 libSBML $as_me 5.15.2, which was
+This file was extended by libSBML $as_me 5.16.0, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
   CONFIG_FILES    = $CONFIG_FILES
@@ -27718,7 +27716,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-libSBML config.status 5.15.2
+libSBML config.status 5.16.0
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"

configure.ac

@@ -50,7 +50,7 @@ AC_INIT([libSBML],
 
 AC_CONFIG_AUX_DIR(config)
 
-AC_REVISION($Revision: 24150 $)
+AC_REVISION($Revision: 24507 $)
 
 AC_CONFIG_SRCDIR(src/Makefile.in)
 
@@ -332,7 +332,7 @@ CONFIG_PROG_SWIG(2.0.0)
 dnl Make sure to test doxygen *after* java, because there's a dependency
 dnl in CONFIG_PROG_DOXYGEN on whether --with-java was also given.
 
-CONFIG_PROG_DOXYGEN(1.7.0,1.8.11)
+CONFIG_PROG_DOXYGEN(1.8.8,1.8.11)
 
 dnl Do this one last, because some earlier config options may end up changing
 dnl things like CFLAGS, which in turn affects the libtool script that the

debian/changelog

+libsbml (5.16.0+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Build-depend on dh-octave instead of octave-pkg-dev (Thanks for the patch
+    to Rafael Laboissière <rafael@debian.org>)
+    Closes: #890089
+  * Standards-Version: 4.1.3
+  * debhelper 11
+  * Adapt docbase files
+  * Remove unused lintian override
+
+ -- Andreas Tille <tille@debian.org>  Sun, 11 Feb 2018 22:54:57 +0100
+
 libsbml (5.15.2+dfsg-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-10
+11

debian/control

@@ -6,7 +6,7 @@ Section: science
 Priority: optional
 Build-Depends: autoconf,
                automake,
-               debhelper (>= 10),
+               debhelper (>= 11~),
                cmake,
                doxygen,
                swig,
@@ -15,7 +15,7 @@ Build-Depends: autoconf,
                perl,
                libperl-dev,
                default-jdk,
-               octave-pkg-dev,
+               dh-octave,
                r-base-dev,
                r-base-core,
                graphviz,
@@ -26,7 +26,7 @@ Build-Depends: autoconf,
                cli-common-dev,
                mono-runtime-common,
                texlive-latex-base
-Standards-Version: 4.0.0
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libsbml.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libsbml.git
 Homepage: http://www.sbml.org/
@@ -111,7 +111,7 @@ Architecture: any
 Section: math
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         octave
+         ${octave:Depends}
 Provides: libsbml-octave
 Description: System Biology Markup Language library - Octave bindings
  LibSBML is a library designed to help you read, write, manipulate,

debian/libsbml5-cil-doc.doc-base

@@ -8,5 +8,5 @@ Abstract: System Biology Markup Language library
 Section: Programming
 
 Format: HTML
-Files: /usr/share/doc/libsbml5-cil-doc/csharp-api/*.html
-Index: /usr/share/doc/libsbml5-cil-doc/csharp-api/index.html
+Files: /usr/share/doc/libsbml5-cil/csharp-api/*.html
+Index: /usr/share/doc/libsbml5-cil/csharp-api/index.html

debian/libsbml5-doc.doc-base

@@ -8,5 +8,5 @@ Abstract: System Biology Markup Language library
 Section: Science/Biology
 
 Format: HTML
-Files: /usr/share/doc/libsbml5-doc/*api/ /usr/share/doc/libsbml5-doc/index.html
-Index: /usr/share/doc/libsbml5-doc/index.html
+Files: /usr/share/doc/libsbml5/*api/ /usr/share/doc/libsbml5/index.html
+Index: /usr/share/doc/libsbml5/index.html

debian/libsbml5-java-doc.doc-base

@@ -8,5 +8,5 @@ Abstract: System Biology Markup Language library
 Section: Programming/Java
 
 Format: HTML
-Files: /usr/share/doc/libsbml5-java-doc/java-api/*.html
-Index: /usr/share/doc/libsbml5-java-doc/java-api/index.html
+Files: /usr/share/doc/libsbml5-java/java-api/*.html
+Index: /usr/share/doc/libsbml5-java/java-api/index.html

debian/libsbml5-java.docs

-debian/tmp/usr/share/doc/libsbml-*/java.txt

debian/libsbml5-perl-doc.doc-base

@@ -8,5 +8,5 @@ Abstract: System Biology Markup Language library
 Section: Programming/Perl
 
 Format: HTML
-Files: /usr/share/doc/libsbml5-perl-doc/perl-api/*.html
-Index: /usr/share/doc/libsbml5-perl-doc/perl-api/index.html
+Files: /usr/share/doc/libsbml5-perl/perl-api/*.html
+Index: /usr/share/doc/libsbml5-perl/perl-api/index.html

debian/libsbml5-python-doc.doc-base

@@ -8,5 +8,5 @@ Abstract: System Biology Markup Language library
 Section: Programming/Python
 
 Format: HTML
-Files: /usr/share/doc/libsbml5-python-doc/python-api/*.html
-Index: /usr/share/doc/libsbml5-python-doc/python-api/index.html
+Files: /usr/share/doc/libsbml5-python/python-api/*.html
+Index: /usr/share/doc/libsbml5-python/python-api/index.html

debian/libsbml5-python.docs

-debian/tmp/usr/share/doc/libsbml-*/python.txt