diff --git a/DESCRIPTION b/DESCRIPTION
index dba45ba5d2a64f020c77931a75e7d90e3b8efb32..a46a8fadbfcd2b5899b420b9d55f380ea899d004 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,21 +1,22 @@
Package: sybilSBML
Type: Package
Title: SBML Integration in Package 'Sybil'
-Version: 3.0.1
-Date: 2016-12-16
+Version: 3.0.2
+Date: 2017-01-12
Authors@R: c(person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
person("Gabriel", "Gelius-Dietrich", role = c("aut", "ctb")),
person("Deya", "Alzoubi", role = "ctb"),
person("Ardalan", "Habil", role = "ctb"))
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Depends: R (>= 2.14.2), Matrix, sybil (>= 2.0.0)
+SystemRequirements: libSBML-core-plus-packages (>= 5.13)
Imports: methods
Description: 'SBML' (Systems Biology Markup Language) with FBC (Flux Balance Constraints) integration in 'sybil'. Many constraint based metabolic models are published in 'SBML' format ('*.xml'). Herewith is the ability to read, write, and check 'SBML' files in 'sybil' provided.
License: GPL-3 | file LICENSE
LazyLoad: yes
Collate: generics.R sbmlPtrClass.R sbmlErrorClass.R sybilSBML.R
uglyHack.R readSBMLmod.R zzz.R
-Packaged: 2016-12-16 07:11:55 UTC; jonathan
+Packaged: 2017-01-12 07:11:55 UTC; jonathan
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut, ctb],
Deya Alzoubi [ctb],
diff --git a/configure b/configure
index ba94dc2b4ec2da43b77e94e9fe8036692a4e4aab..fcafb4878f08f5ff429bf1d920e831ffc8f49ae7 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for sybilSBML 3.0.0.
+# Generated by GNU Autoconf 2.69 for sybilSBML 3.0.2.
#
# Report bugs to <clausjonathan.fritzemeier@uni-duesseldorf.de>.
#
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='sybilSBML'
PACKAGE_TARNAME='sybilsbml'
-PACKAGE_VERSION='3.0.0'
-PACKAGE_STRING='sybilSBML 3.0.0'
+PACKAGE_VERSION='3.0.2'
+PACKAGE_STRING='sybilSBML 3.0.2'
PACKAGE_BUGREPORT='clausjonathan.fritzemeier@uni-duesseldorf.de'
PACKAGE_URL=''
@@ -1230,7 +1230,7 @@ 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 sybilSBML 3.0.0 to adapt to many kinds of systems.
+\`configure' configures sybilSBML 3.0.2 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1291,7 +1291,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of sybilSBML 3.0.0:";;
+ short | recursive ) echo "Configuration of sybilSBML 3.0.2:";;
esac
cat <<\_ACEOF
@@ -1378,7 +1378,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-sybilSBML configure 3.0.0
+sybilSBML configure 3.0.2
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1747,7 +1747,7 @@ 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 sybilSBML $as_me 3.0.0, which was
+It was created by sybilSBML $as_me 3.0.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -3650,7 +3650,7 @@ if test "x$ac_cv_header_sbml_packages_fbc_common_FbcExtensionTypes_h" = xyes; th
else
as_fn_error $? "Could not find specific FBC header of libSBML:
- make sure your libSBML version is >= 5.13." "$LINENO" 5
+ make sure your libSBML version is >= 5.13 and including the FBC package." "$LINENO" 5
fi
@@ -3670,7 +3670,7 @@ _ACEOF
else
as_fn_error $? "Could not find specific FBC function of libSBML:
- make sure your libSBML version is >= 5.13." "$LINENO" 5
+ make sure your libSBML version is >= 5.13 and including the FBC package." "$LINENO" 5
fi
done
@@ -4239,7 +4239,7 @@ cat >>$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 sybilSBML $as_me 3.0.0, which was
+This file was extended by sybilSBML $as_me 3.0.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -4292,7 +4292,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-sybilSBML config.status 3.0.0
+sybilSBML config.status 3.0.2
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index 08faede40197a400f9e86fc8520a65aa90f60143..060f6932c14f14f33e2e6a280c9e5f51d487e3f2 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([sybilSBML], [3.0.0], [clausjonathan.fritzemeier@uni-duesseldorf.de])
+AC_INIT([sybilSBML], [3.0.2], [clausjonathan.fritzemeier@uni-duesseldorf.de])
dnl # --------------------------------------------------------------------
dnl # global (environment) variables
@@ -242,7 +242,7 @@ AC_CHECK_LIB([sbml], [readSBML], ,
AC_CHECK_HEADER([sbml/packages/fbc/common/FbcExtensionTypes.h], ,
AC_MSG_ERROR([Could not find specific FBC header of libSBML:
- make sure your libSBML version is >= 5.13.]),
+ make sure your libSBML version is >= 5.13 and including the FBC package.]),
[#include <sbml/SBMLTypes.h>])
#AC_CHECK_LIB([sbml], [SBMLExtensionRegistry_getRegisteredPackages], ,
@@ -251,7 +251,7 @@ AC_CHECK_HEADER([sbml/packages/fbc/common/FbcExtensionTypes.h], ,
AC_CHECK_FUNCS([SBase_getPlugin SBMLExtensionRegistry_getRegisteredPackages GeneProductAssociation_setAssociation FbcReactionPlugin_getLowerFluxBound], ,
AC_MSG_ERROR([Could not find specific FBC function of libSBML:
- make sure your libSBML version is >= 5.13.]))
+ make sure your libSBML version is >= 5.13 and including the FBC package.]))
#AC_SEARCH_LIBS([SBase_getPlugin], [sbml], ,
# AC_MSG_ERROR([Could not find specific FBC function of libSBML:
diff --git a/inst/INSTALL b/inst/INSTALL
index 1036d3ce5af87533b7ca92e8a41ece51692f3354..e1a306bf9ccff263b5fd59d54dcb696d33c1a381 100644
--- a/inst/INSTALL
+++ b/inst/INSTALL
@@ -1,10 +1,19 @@
GNU R package sybilSBML: Link to libSBML for sybil
+# ---------------------------------------------------------------------------- #
+# All Systems
+# ---------------------------------------------------------------------------- #
+
+First make sure you have installed libsbml >= 5.13 with the FBC package. At
+http://sbml.org/Software/libSBML you can find installers for various plattforms
+and the source to compile by yourself. In this case download the file
+libSBML-5.13.0-core-plus-packages-src.* from their sourceforge page and use the
+configure option "--enable-fbc".
+
The installation procedure for the sybilSBML package needs to know where to
find the libSBML include directory and where to find the callable library.
-
# ---------------------------------------------------------------------------- #
# Linux and MacOS X installation
# ---------------------------------------------------------------------------- #
diff --git a/inst/README b/inst/README
index 543e28aedcbdb595d13fa5ed130c0c9f418db94b..b82fb4f1409b9fee968f2fc7d01b997a9f957f64 100644
--- a/inst/README
+++ b/inst/README
@@ -1,4 +1,4 @@
GNU R package sybilSBML: Link to libSBML for sybil
-The package sybilSBML requires a working installation of libSBML (>= 5.6.0)
-(in particular libraries and header files).
+The package sybilSBML requires a working installation of libSBML (>= 5.13.0)
+(in particular libraries and header files with the FBC package).