The package rpms/COPASI.git has added or updated architecture specific content in its
spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s):
https://src.fedoraproject.org/cgit/rpms/COPASI.git/commit/?id=361b3ed5cb9...
https://src.fedoraproject.org/cgit/rpms/COPASI.git/commit/?id=9636c73d63a....
Change:
-%ifarch %{ix86} x86_64 sparc sparcv9 ia64 %{arm} aarch64 alpha s390x ppc
-%ifarch %{openblas_arches}
Thanks.
Full change:
============
commit 361b3ed5cb9a0e0fdc36ed75d021ac8c2a76efcc
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Thu Aug 1 19:02:05 2019 +0200
Release 4.25 build-213
diff --git a/.gitignore b/.gitignore
index 4a58bf0..06adb90 100644
--- a/.gitignore
+++ b/.gitignore
@@ -24,3 +24,4 @@
/COPASI-Build-184.tar.gz
/COPASI-Build-197.tar.gz
/COPASI-Build-207.tar.gz
+/COPASI-Build-213.tar.gz
diff --git a/COPASI-use_c++17.patch b/COPASI-use_c++17.patch
new file mode 100644
index 0000000..c7647af
--- /dev/null
+++ b/COPASI-use_c++17.patch
@@ -0,0 +1,14 @@
+--- CMakeLists.txt_use_cxx17 2019-07-29 10:31:06.000000000 +0200
++++ CMakeLists.txt 2019-07-31 19:04:52.285195735 +0200
+@@ -118,9 +118,9 @@
+ endif()
+
+ if (CMAKE_MAJOR_VERSION LESS 3 OR CMAKE_MINOR_VERSION LESS 1)
+- set(CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} "-std=c++11")
++ set(CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} "-std=gnu++17")
+ else()
+- set(CMAKE_CXX_STANDARD 11)
++ set(CMAKE_CXX_STANDARD 17)
+ endif()
+
+ CHECK_FUNCTION_EXISTS(strptime HAVE_STRPTIME)
diff --git a/COPASI.rpmlintrc b/COPASI.rpmlintrc
deleted file mode 100644
index ad480d2..0000000
--- a/COPASI.rpmlintrc
+++ /dev/null
@@ -1,18 +0,0 @@
-# Whitelisting errors
-#
https://fedoraproject.org/wiki/Taskotron/Tasks/dist.rpmlint#whitelist
-
-# Edited by sagitter (sagitter AT fedoraproject dot org)
-
-# KNOWN BUGS:
-#
-
-# TESTS:
-##### SRPMs #####
-
-addFilter(r'(hardcoded-library-path) %{_prefix}/lib/mono/copasicsP')
-
-# WARNINGS:
-##### RPMs #####
-addFilter(r'(no-manual-page-for-binary) CopasiSE')
-addFilter(r'(no-manual-page-for-binary) CopasiUI')
-addFilter(r'(no-manual-page-for-binary) CopasiSBW')
diff --git a/COPASI.spec b/COPASI.spec
index f4032b1..d528f7f 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -1,38 +1,17 @@
-%global buildid 207
-%global octpkg COPASI
+%global buildid 213
+%global octpkg COPASI
%global with_python 1
-# Disable Java binding
+# Disabled bindings
%global with_java 0
-
-# Disable Octave binding ('virtual memory exhausted' issue)
%global with_octave 0
-
-%global with_perl 1
-%global with_r 1
-
-# rhbz #1588734,#1686738
-%if 0%{?fedora} && 0%{?fedora} < 30
-%ifarch %{?mono_arches}
-%global with_mono 1
-%else
+%global with_perl 0
+%global with_r 0
%global with_mono 0
-%endif
-%endif
-
-%if 0%{?fedora} && 0%{?fedora} >= 30
-%ifarch %{ix86} x86_64 sparc sparcv9 ia64 %{arm} aarch64 alpha s390x ppc
-%global with_mono 1
-%else
-%global with_mono 0
-
-Obsoletes: COPASI-sharp < 4.24.197-7
-%endif
-%endif
#
-##Use QWT6? (Experimental)
+# Use QWT6? (Experimental)
%global with_qwt6 0
%if 0%{?with_octave}
@@ -46,7 +25,7 @@ Obsoletes: COPASI-sharp < 4.24.197-7
Name: COPASI
Summary: Biochemical network simulator
Version: 4.25.%{buildid}
-Release: 6%{?dist}
+Release: 1%{?dist}
##Artistic 2.0 is main license
##GPLv2+ is related to a Mixed Source Licensing Scenario
@@ -102,32 +81,37 @@ BuildRequires: minizip-devel
Requires: %{name}-data = %{version}-%{release}
Requires: libsedml%{?_isa} >= 1:0.4.3-3
-Obsoletes: python2-%{name} < 4.24.197
+Obsoletes: R-%{octpkg} < 0:4.25.213-1
+Obsoletes: perl-%{octpkg} < 0:4.25.213-1
+Obsoletes: %{name}-sharp < 0:4.25.213-1
-##This patch sets libraries' installation paths
+# This patch sets libraries' installation paths
Patch0: %{name}-fix_install_libpaths.patch
-##This patch sets paths to find QWT5, QTMML, SBW files on Fedora
+# This patch sets paths to find QWT5, QTMML, SBW files on Fedora
Patch1: %{name}-find_QWT5-QTMML-SBW.patch
-##This patch sets paths to find QWT6, QTMML, SBW files on Fedora
+# This patch sets paths to find QWT6, QTMML, SBW files on Fedora
Patch3: %{name}-find_QWT6-QTMML-SBW.patch
-##This patch sets paths to find QTPLOT3D-QT4 files on Fedora
+# This patch sets paths to find QTPLOT3D-QT4 files on Fedora
Patch2: %{name}-set_QWTPLOT3D_QT4.patch
-##This patch fixes executable permissions of CopasiSE and CopasiUI
+# This patch fixes executable permissions of CopasiSE and CopasiUI
Patch4: %{name}-fix_exe_permissions.patch
-##This patch sets paths to find QTPLOT3D-QT5 files on Fedora
+# This patch sets paths to find QTPLOT3D-QT5 files on Fedora
Patch5: %{name}-set_QWTPLOT3D_QT5.patch
-##This patch sets paths to find libCombine files on Fedora
+# This patch sets paths to find libCombine files on Fedora
Patch6: %{name}-libCombine_paths.patch
-##This patch sets paths to find libcroosguid2 files on Fedora
+# This patch sets paths to find libcroosguid2 files on Fedora
Patch7: %{name}-find_crossguid2.patch
+# This patch forces the use of C++17 standard
+Patch8: %{name}-use_c++17.patch
+
%description
COPASI is a software application for simulation and analysis of biochemical
networks and their dynamics.
@@ -171,7 +155,7 @@ This package provides the COPASI data, example and license files.
%package -n python3-%{name}
Summary: %{name} Python3 Bindings
BuildRequires: python3-devel
-Obsoletes: python2-%{name} < 4.24.197
+Obsoletes: python2-%{name}
%{?python_provide:%python_provide python3-%{name}}
%description -n python3-%{octpkg}
This package provides the libraries to
@@ -258,6 +242,7 @@ done
%patch4 -p0 -b .fix_exe_permissions
%patch6 -p0 -b .libCombine_paths
%patch7 -p0 -b .find_crossguid2
+%patch8 -p0 -b .use_c++17
%if 0%{?with_qwt6}
%patch3 -p0
@@ -265,18 +250,28 @@ done
%patch1 -p0
%endif
-##Set Qwt libdir
+# Set Qwt libdir
sed -e 's|@@libdir@@|%{_libdir}|g' -i CMakeModules/FindQwtQt4.cmake
%patch5 -p0
-####Set QTPLOT3D-QT5 paths
+# Set QTPLOT3D-QT5 paths
sed -e 's|@@qtplot3d_includedir@@|%{_qt5_headerdir}/qwtplot3d-qt5|g' -i
CMakeModules/FindQwtplot3dQt4.cmake
sed -e 's|@@qtplot3d_libdir@@|%{_qt5_libdir}|g' -i
CMakeModules/FindQwtplot3dQt4.cmake
-##Set QtMmlQt5 paths
+# Set QtMmlQt5 paths
sed -e 's|@@_libmml_includedir@@|%{_qt5_headerdir}/libmml-qt5|g' -i
CMakeModules/FindQtMmlQt4.cmake
sed -e 's|@@_libmml_libdir@@|%{_qt5_libdir}|g' -i
CMakeModules/FindQtMmlQt4.cmake
+# Exclude obsolete functions
+#
http://tracker.copasi.org/show_bug.cgi?id=2810#c1
+sed -i.bak '/double sqrt(doublereal);/d' copasi/optimization/CNL2SOL.cpp
+sed -i.bak '/double pow_dd(doublereal *, doublereal *);/d'
copasi/optimization/CNL2SOL.cpp
+sed -i.bak '/int s_copy(char *, char *, ftnlen, ftnlen);/d'
copasi/optimization/CNL2SOL.cpp
+sed -i.bak '/double sqrt(doublereal);/d' copasi/odepack++/dc_decsol.cpp
+sed -i.bak '/double sqrt(doublereal),/d' copasi/odepack++/CRadau5.cpp
+sed -i.bak '/double pow_dd(doublereal *,/d' copasi/odepack++/CRadau5.cpp
+sed -i.bak '/C_FLOAT64 d_lg10(C_FLOAT64 *);/d' copasi/optimization/CPraxis.cpp
+
%build
mkdir -p build && pushd build
export CXXFLAGS="-I$PWD/../copasi/lapack -DF2C_INTEGER=int -DF2C_LOGICAL=long
%{optflags} %{__global_ldflags}"
@@ -353,7 +348,7 @@ popd
rm -rf $RPM_BUILD_ROOT%{python3_sitearch}/copasi/examples
%endif
-##Just for R library
+# For R library only
%if 0%{?with_r}
mkdir -p $RPM_BUILD_ROOT%{_libdir}/R/library
%{_bindir}/R CMD INSTALL -l $RPM_BUILD_ROOT%{_libdir}/R/library
build/copasi/bindings/R/%{name}_*.tar.gz
@@ -367,10 +362,10 @@ mkdir -p $RPM_BUILD_ROOT%{octpkgdir}/packinfo
install -pm 644 copasi/ArtisticLicense.txt $RPM_BUILD_ROOT%{octpkgdir}/packinfo
%endif
-##Install .xpm icon files
+# Install .xpm icon files
install -pm 644 copasi/UI/icons/Copasi48-Alpha.xpm
$RPM_BUILD_ROOT%{_datadir}/icons/copasi/icons
-##Make a .desktop file
+# Make a .desktop file
mkdir -p $RPM_BUILD_ROOT%{_datadir}/applications
cat > $RPM_BUILD_ROOT%{_datadir}/applications/%{name}.desktop <<EOF
[Desktop Entry]
@@ -384,7 +379,7 @@ Type=Application
Categories=Science;
EOF
-## Install appdata file
+# Install appdata file
mkdir -p $RPM_BUILD_ROOT%{_metainfodir}
install -pm 644 %{SOURCE1} $RPM_BUILD_ROOT%{_metainfodir}/
@@ -452,6 +447,12 @@ appstream-util validate-relax --nonet
$RPM_BUILD_ROOT%{_metainfodir}/*.appdata.x
%{_datadir}/copasi/doc/
%changelog
+* Wed Jul 31 2019 Antonio Trande <sagitterATfedoraproject.org> - 4.25.213-1
+- Release 4.25 build-213
+- Use standard c++17
+- Disable R package
+- Disable perl package
+
* Wed Jun 19 2019 Tim Landscheidt <tim(a)tim-landscheidt.de> - 4.25.207-6
- Do not list Git-tracked COPASI.rpmlintrc as source
diff --git a/sources b/sources
index dc418ef..d8328a6 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (COPASI-Build-207.tar.gz) =
eda3c4416912f73849b701c60accf4a1f49317623ba23fea3d4dc6a437b2417a91ae71b9bafa448b57d3ce0e1928b078593b75acdd9bc8ddc9d3973683130603
+SHA512 (COPASI-Build-213.tar.gz) =
8cfa7a6d4e4b026dca900f09a75afcb670d03c341dc3f36833e58021efe5edc4e29c5d81ff20be80acca39a5afeb112bd0fcedbaf37206bad8e9015155dbd4a8
commit 64ddcf034cf1963852fdbd4f1e2526ebcfbced63
Author: Tim Landscheidt <tim(a)tim-landscheidt.de>
Date: Wed Jun 19 08:40:21 2019 +0000
Do not list Git-tracked COPASI.rpmlintrc as source
diff --git a/COPASI.rpmlintrc b/COPASI.rpmlintrc
index f127f75..ad480d2 100644
--- a/COPASI.rpmlintrc
+++ b/COPASI.rpmlintrc
@@ -1,3 +1,6 @@
+# Whitelisting errors
+#
https://fedoraproject.org/wiki/Taskotron/Tasks/dist.rpmlint#whitelist
+
# Edited by sagitter (sagitter AT fedoraproject dot org)
# KNOWN BUGS:
diff --git a/COPASI.spec b/COPASI.spec
index 9902afc..f4032b1 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -46,7 +46,7 @@ Obsoletes: COPASI-sharp < 4.24.197-7
Name: COPASI
Summary: Biochemical network simulator
Version: 4.25.%{buildid}
-Release: 5%{?dist}
+Release: 6%{?dist}
##Artistic 2.0 is main license
##GPLv2+ is related to a Mixed Source Licensing Scenario
@@ -61,10 +61,6 @@ URL:
http://copasi.org/
Source0:
https://github.com/copasi/COPASI/archive/Build-%{buildid}/%{name}-Build-%...
Source1: %{name}.appdata.xml
-# Whitelisting errors
-#
https://fedoraproject.org/wiki/Taskotron/Tasks/dist.rpmlint#whitelist
-Source2: %{name}.rpmlintrc
-
%if 0%{?with_qwt6}
BuildRequires: qwt-devel
%endif
@@ -456,6 +452,9 @@ appstream-util validate-relax --nonet
$RPM_BUILD_ROOT%{_metainfodir}/*.appdata.x
%{_datadir}/copasi/doc/
%changelog
+* Wed Jun 19 2019 Tim Landscheidt <tim(a)tim-landscheidt.de> - 4.25.207-6
+- Do not list Git-tracked COPASI.rpmlintrc as source
+
* Tue Jun 18 2019 Orion Poplawski <orion(a)nwra.com> - 4.25.207-5
- Rebuild for octave 5.1
commit af241e4b822670e5c15da15f1f51d2ad53c3f5cd
Author: Orion Poplawski <orion(a)nwra.com>
Date: Mon Jun 17 21:30:35 2019 -0600
Rebuild for octave 5.1
diff --git a/COPASI.spec b/COPASI.spec
index 100b08c..9902afc 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -46,7 +46,7 @@ Obsoletes: COPASI-sharp < 4.24.197-7
Name: COPASI
Summary: Biochemical network simulator
Version: 4.25.%{buildid}
-Release: 4%{?dist}
+Release: 5%{?dist}
##Artistic 2.0 is main license
##GPLv2+ is related to a Mixed Source Licensing Scenario
@@ -90,6 +90,8 @@ BuildRequires: libxslt-devel
BuildRequires: pkgconf-pkg-config
BuildRequires: openblas-devel, openblas-srpm-macros, lapack-devel
BuildRequires: crossguid2-devel >= 0:0.2.2
+# Needed until
https://bugzilla.redhat.com/show_bug.cgi?id=1721342 is resolved
+BuildRequires: libuuid-devel
BuildRequires: desktop-file-utils
BuildRequires: swig
BuildRequires: expat-devel
@@ -454,6 +456,9 @@ appstream-util validate-relax --nonet
$RPM_BUILD_ROOT%{_metainfodir}/*.appdata.x
%{_datadir}/copasi/doc/
%changelog
+* Tue Jun 18 2019 Orion Poplawski <orion(a)nwra.com> - 4.25.207-5
+- Rebuild for octave 5.1
+
* Sat Jun 01 2019 Jitka Plesnikova <jplesnik(a)redhat.com> - 4.25.207-4
- Perl 5.30 rebuild
commit e0d83d74a24f8acb41d2e07e04fc96b22050c37e
Author: Jitka Plesnikova <jplesnik(a)redhat.com>
Date: Sat Jun 1 20:20:57 2019 +0200
Perl 5.30 rebuild
diff --git a/COPASI.spec b/COPASI.spec
index 2ecae8b..100b08c 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -46,7 +46,7 @@ Obsoletes: COPASI-sharp < 4.24.197-7
Name: COPASI
Summary: Biochemical network simulator
Version: 4.25.%{buildid}
-Release: 3%{?dist}
+Release: 4%{?dist}
##Artistic 2.0 is main license
##GPLv2+ is related to a Mixed Source Licensing Scenario
@@ -454,6 +454,9 @@ appstream-util validate-relax --nonet
$RPM_BUILD_ROOT%{_metainfodir}/*.appdata.x
%{_datadir}/copasi/doc/
%changelog
+* Sat Jun 01 2019 Jitka Plesnikova <jplesnik(a)redhat.com> - 4.25.207-4
+- Perl 5.30 rebuild
+
* Tue May 21 2019 Antonio Trande <sagitterATfedoraproject.org> - 4.25.207-3
- Use Python3 abiflags
commit cafae5b07a148eaa5d188c6926d843739f6b3847
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Tue May 21 19:09:40 2019 +0200
Fix python3-config commands again
diff --git a/COPASI.spec b/COPASI.spec
index a7b586f..2ecae8b 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -287,8 +287,8 @@ export CXXFLAGS="-I$PWD/../copasi/lapack -DF2C_INTEGER=int
-DF2C_LOGICAL=long %{
%if 0%{?with_python}
-DENABLE_PYTHON:BOOL=ON \
-DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \
- -DPYTHON_INCLUDE_DIR:PATH=%{_includedir}/python%{python3_version}${python3-config
--abiflags} \
- -DPYTHON_LIBRARY:FILEPATH=%{_libdir}/libpython%{python3_version}${python3-config
--abiflags}.so \
+ -DPYTHON_INCLUDE_DIR:PATH=%{_includedir}/python%{python3_version}%(python3-config
--abiflags) \
+ -DPYTHON_LIBRARY:FILEPATH=%{_libdir}/libpython%{python3_version}%(python3-config
--abiflags).so \
%else
-DENABLE_PYTHON:BOOL=OFF \
%endif
commit a39081947b8ae474eb2a7e023218d7f230b88dad
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Tue May 21 18:50:26 2019 +0200
Fix python3-config commands
diff --git a/COPASI.spec b/COPASI.spec
index 16f25b3..a7b586f 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -287,8 +287,8 @@ export CXXFLAGS="-I$PWD/../copasi/lapack -DF2C_INTEGER=int
-DF2C_LOGICAL=long %{
%if 0%{?with_python}
-DENABLE_PYTHON:BOOL=ON \
-DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \
- -DPYTHON_INCLUDE_DIR:PATH=%{_includedir}/python%{python3_version}%{python3-config
--abiflags} \
- -DPYTHON_LIBRARY:FILEPATH=%{_libdir}/libpython%{python3_version}%{python3-config
--abiflags}.so \
+ -DPYTHON_INCLUDE_DIR:PATH=%{_includedir}/python%{python3_version}${python3-config
--abiflags} \
+ -DPYTHON_LIBRARY:FILEPATH=%{_libdir}/libpython%{python3_version}${python3-config
--abiflags}.so \
%else
-DENABLE_PYTHON:BOOL=OFF \
%endif
commit 4df7a86e1a789daec0dfb656cf86b58afa0623c7
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Tue May 21 18:43:49 2019 +0200
Use Python3 abiflags
diff --git a/COPASI.spec b/COPASI.spec
index cad56a3..16f25b3 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -46,7 +46,7 @@ Obsoletes: COPASI-sharp < 4.24.197-7
Name: COPASI
Summary: Biochemical network simulator
Version: 4.25.%{buildid}
-Release: 2%{?dist}
+Release: 3%{?dist}
##Artistic 2.0 is main license
##GPLv2+ is related to a Mixed Source Licensing Scenario
@@ -287,8 +287,8 @@ export CXXFLAGS="-I$PWD/../copasi/lapack -DF2C_INTEGER=int
-DF2C_LOGICAL=long %{
%if 0%{?with_python}
-DENABLE_PYTHON:BOOL=ON \
-DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \
- -DPYTHON_INCLUDE_DIR:PATH=%{_includedir}/python%{python3_version}m \
- -DPYTHON_LIBRARY:FILEPATH=%{_libdir}/libpython%{python3_version}m.so \
+ -DPYTHON_INCLUDE_DIR:PATH=%{_includedir}/python%{python3_version}%{python3-config
--abiflags} \
+ -DPYTHON_LIBRARY:FILEPATH=%{_libdir}/libpython%{python3_version}%{python3-config
--abiflags}.so \
%else
-DENABLE_PYTHON:BOOL=OFF \
%endif
@@ -454,6 +454,9 @@ appstream-util validate-relax --nonet
$RPM_BUILD_ROOT%{_metainfodir}/*.appdata.x
%{_datadir}/copasi/doc/
%changelog
+* Tue May 21 2019 Antonio Trande <sagitterATfedoraproject.org> - 4.25.207-3
+- Use Python3 abiflags
+
* Sun May 05 2019 Antonio Trande <sagitterATfedoraproject.org> - 4.25.207-2
- Rebuild for libsbml-5.18.0
commit c25b88cba9794c3c8e26df7a054a33daf5cd5848
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Sun May 5 19:33:18 2019 +0200
Rebuild for libsbml-5.18.0
diff --git a/COPASI.spec b/COPASI.spec
index 80ab596..cad56a3 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -1,7 +1,7 @@
-%global buildid 207
+%global buildid 207
%global octpkg COPASI
-%global with_python3 1
+%global with_python 1
# Disable Java binding
%global with_java 0
@@ -46,7 +46,7 @@ Obsoletes: COPASI-sharp < 4.24.197-7
Name: COPASI
Summary: Biochemical network simulator
Version: 4.25.%{buildid}
-Release: 1%{?dist}
+Release: 2%{?dist}
##Artistic 2.0 is main license
##GPLv2+ is related to a Mixed Source Licensing Scenario
@@ -169,7 +169,7 @@ BuildArch: noarch
%description data
This package provides the COPASI data, example and license files.
-%if 0%{?with_python3}
+%if 0%{?with_python}
%package -n python3-%{name}
Summary: %{name} Python3 Bindings
BuildRequires: python3-devel
@@ -284,7 +284,7 @@ mkdir -p build && pushd build
export CXXFLAGS="-I$PWD/../copasi/lapack -DF2C_INTEGER=int -DF2C_LOGICAL=long
%{optflags} %{__global_ldflags}"
%cmake -Wno-dev \
-DCOPASI_OVERRIDE_VERSION:STRING=%{version} \
-%if 0%{?with_python3}
+%if 0%{?with_python}
-DENABLE_PYTHON:BOOL=ON \
-DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \
-DPYTHON_INCLUDE_DIR:PATH=%{_includedir}/python%{python3_version}m \
@@ -351,7 +351,7 @@ popd
%make_install -C build
# Remove directory of examples
-%if 0%{?with_python3}
+%if 0%{?with_python}
rm -rf $RPM_BUILD_ROOT%{python3_sitearch}/copasi/examples
%endif
@@ -409,7 +409,7 @@ appstream-util validate-relax --nonet
$RPM_BUILD_ROOT%{_metainfodir}/*.appdata.x
%{_datadir}/copasi/
%exclude %{_datadir}/copasi/doc/
-%if 0%{?with_python3}
+%if 0%{?with_python}
%files -n python3-%{octpkg}
%license copasi/ArtisticLicense.txt
%{python3_sitearch}/copasi/
@@ -454,6 +454,9 @@ appstream-util validate-relax --nonet
$RPM_BUILD_ROOT%{_metainfodir}/*.appdata.x
%{_datadir}/copasi/doc/
%changelog
+* Sun May 05 2019 Antonio Trande <sagitterATfedoraproject.org> - 4.25.207-2
+- Rebuild for libsbml-5.18.0
+
* Sat Mar 16 2019 Antonio Trande <sagitterATfedoraproject.org> - 4.25.207-1
- Release 4.25 build-207
- Use openblas always
commit 9636c73d63a4c7b1fab4724950dd92429f503d41
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Mon Mar 25 17:48:36 2019 +0100
Release 4.25 build-207|Use openblas always
diff --git a/.gitignore b/.gitignore
index 9d1e74f..4a58bf0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -23,3 +23,4 @@
/COPASI-Build-170.tar.gz
/COPASI-Build-184.tar.gz
/COPASI-Build-197.tar.gz
+/COPASI-Build-207.tar.gz
diff --git a/COPASI-find_crossguid2.patch b/COPASI-find_crossguid2.patch
new file mode 100644
index 0000000..137971c
--- /dev/null
+++ b/COPASI-find_crossguid2.patch
@@ -0,0 +1,56 @@
+--- CMakeModules/FindCROSSGUID.orig.cmake 2019-03-23 19:54:03.269453000 +0100
++++ CMakeModules/FindCROSSGUID.cmake 2019-03-23 19:56:45.218630640 +0100
+@@ -16,11 +16,11 @@
+ # $CROSSGUID_DIR is an environment variable that would
+ # correspond to the ./configure --prefix=$CROSSGUID_DIR
+
+-find_package(crossguid CONFIG REQUIRED
+- CONFIGS crossguid-config.cmake
++find_package(crossguid2 CONFIG REQUIRED
++ CONFIGS crossguid2-config.cmake
+ PATHS $ENV{CROSSGUID_DIR}/${CMAKE_INSTALL_LIBDIR}/cmake
+ ${COPASI_DEPENDENCY_DIR}/${CMAKE_INSTALL_LIBDIR}/cmake
+- /usr/${CMAKE_INSTALL_LIBDIR}/cmake
++ ${CMAKE_INSTALL_LIBDIR}/cmake/crossguid2
+ )
+
+ if (NOT CROSSGUID_FOUND)
+@@ -29,6 +29,7 @@
+ find_path(CROSSGUID_INCLUDE_DIR crossguid/guid.hpp
+ PATHS $ENV{CROSSGUID_DIR}/include
+ $ENV{CROSSGUID_DIR}
++ ${INCLUDE_INSTALL_DIR}/crossguid2
+ ${COPASI_DEPENDENCY_DIR}/include
+ ${COPASI_DEPENDENCY_DIR}
+ ~/Library/Frameworks
+@@ -45,10 +46,10 @@
+ endif (NOT CROSSGUID_INCLUDE_DIR)
+
+ find_library(CROSSGUID_LIBRARY
+- NAMES crossguid crossguid-dgb
++ NAMES crossguid2 crossguid-dgb
+ PATHS $ENV{CROSSGUID_DIR}/lib
+ $ENV{CROSSGUID_DIR}
+- ${COPASI_DEPENDENCY_DIR}/${CMAKE_INSTALL_LIBDIR}
++ ${CMAKE_INSTALL_LIBDIR}
+ ${COPASI_DEPENDENCY_DIR}/lib
+ ${COPASI_DEPENDENCY_DIR}
+ ~/Library/Frameworks
+@@ -73,14 +74,14 @@
+ else ()
+ set(CROSSGUID_FOUND ${crossguid_FOUND})
+
+- get_target_property(CROSSGUID_INCLUDE_DIR crossguid INTERFACE_INCLUDE_DIRECTORIES)
+- get_target_property(CROSSGUID_LIBRARY crossguid IMPORTED_LOCATION_RELEASE)
++ get_target_property(CROSSGUID_INCLUDE_DIR crossguid2 INTERFACE_INCLUDE_DIRECTORIES)
++ get_target_property(CROSSGUID_LIBRARY crossguid2 IMPORTED_LOCATION_RELEASE)
+
+ if (NOT CROSSGUID_LIBRARY)
+ get_target_property(CROSSGUID_LIBRARY crossguid IMPORTED_LOCATION_DEBUG)
+ endif()
+
+- get_target_property(CROSSGUID_INTERFACE_LINK_LIBRARIES crossguid
INTERFACE_LINK_LIBRARIES)
++ get_target_property(CROSSGUID_INTERFACE_LINK_LIBRARIES crossguid2
INTERFACE_LINK_LIBRARIES)
+
+ if (CROSSGUID_INTERFACE_LINK_LIBRARIES)
+ set(CROSSGUID_LIBRARY ${CROSSGUID_LIBRARY} ${CROSSGUID_INTERFACE_LINK_LIBRARIES})
diff --git a/COPASI-fix_install_libpaths.patch b/COPASI-fix_install_libpaths.patch
index 8f03174..c5aabf0 100644
--- a/COPASI-fix_install_libpaths.patch
+++ b/COPASI-fix_install_libpaths.patch
@@ -105,7 +105,7 @@
# they still work with the current objectmodel
--- copasi/bindings/octave/CMakeLists.orig.txt 2015-01-07 15:45:42.000000000 +0100
+++ copasi/bindings/octave/CMakeLists.txt 2015-01-08 18:34:10.609971192 +0100
-@@ -145,12 +145,12 @@
+@@ -147,12 +147,12 @@
#
set(OCTAVE_PACKAGE_INSTALL_DIR)
if (UNIX OR CYGWIN)
@@ -118,5 +118,5 @@
-INSTALL(TARGETS binding_octave_lib DESTINATION ${OCTAVE_PACKAGE_INSTALL_DIR} )
+INSTALL(TARGETS binding_octave_lib PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE
GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE DESTINATION
${OCTAVE_PACKAGE_INSTALL_DIR})
- add_test(NAME octave_test_version
- COMMAND octave --no-gui --eval
"COPASI;display(COPASI.CVersion.VERSION.getVersion())"
+ set(OCTAVE_INTERPRETER "octave" CACHE STRING "full path to the octave
interpreter to be used for running tests." )
+
diff --git a/COPASI.spec b/COPASI.spec
index 164aec8..80ab596 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -1,4 +1,4 @@
-%global buildid 197
+%global buildid 207
%global octpkg COPASI
%global with_python3 1
@@ -26,7 +26,8 @@
%global with_mono 1
%else
%global with_mono 0
-Obsoletes: %{name}-sharp < 4.24.197-7
+
+Obsoletes: COPASI-sharp < 4.24.197-7
%endif
%endif
#
@@ -44,8 +45,8 @@ Obsoletes: %{name}-sharp < 4.24.197-7
Name: COPASI
Summary: Biochemical network simulator
-Version: 4.24.%{buildid}
-Release: 8%{?dist}
+Version: 4.25.%{buildid}
+Release: 1%{?dist}
##Artistic 2.0 is main license
##GPLv2+ is related to a Mixed Source Licensing Scenario
@@ -87,12 +88,8 @@ BuildRequires: cppunit-devel
BuildRequires: libcurl-devel
BuildRequires: libxslt-devel
BuildRequires: pkgconf-pkg-config
-%ifarch %{openblas_arches}
-BuildRequires: openblas-devel, openblas-srpm-macros
-%else
-BuildRequires: blas-devel
-BuildRequires: lapack-devel
-%endif
+BuildRequires: openblas-devel, openblas-srpm-macros, lapack-devel
+BuildRequires: crossguid2-devel >= 0:0.2.2
BuildRequires: desktop-file-utils
BuildRequires: swig
BuildRequires: expat-devel
@@ -102,17 +99,7 @@ BuildRequires: cmake, gcc, gcc-c++
BuildRequires: bison
BuildRequires: ImageMagick
BuildRequires: libappstream-glib
-# Use new minizip starting from fedora 30
-# rhbz #1632172
-%if 0%{?fedora} == 29
-BuildRequires: minizip-compat-devel
-%endif
-%if 0%{?fedora} == 28
-BuildRequires: minizip-devel
-%endif
-%if 0%{?fedora} >= 30
-#BuildRequires: minizip-devel >= 2.5.0
-%endif
+BuildRequires: minizip-devel
Requires: %{name}-data = %{version}-%{release}
Requires: libsedml%{?_isa} >= 1:0.4.3-3
@@ -138,7 +125,10 @@ Patch4: %{name}-fix_exe_permissions.patch
Patch5: %{name}-set_QWTPLOT3D_QT5.patch
##This patch sets paths to find libCombine files on Fedora
-Patch6: COPASI-libCombine_paths.patch
+Patch6: %{name}-libCombine_paths.patch
+
+##This patch sets paths to find libcroosguid2 files on Fedora
+Patch7: %{name}-find_crossguid2.patch
%description
COPASI is a software application for simulation and analysis of biochemical
@@ -266,9 +256,10 @@ for file in `find copasi -type f \( -name "*.cpp" \)`; do
mv $file.new $file
done
-%patch0 -p0
-%patch4 -p0
-%patch6 -p0
+%patch0 -p0 -b .fix_install_libpaths
+%patch4 -p0 -b .fix_exe_permissions
+%patch6 -p0 -b .libCombine_paths
+%patch7 -p0 -b .find_crossguid2
%if 0%{?with_qwt6}
%patch3 -p0
@@ -290,17 +281,7 @@ sed -e 's|@@_libmml_libdir@@|%{_qt5_libdir}|g' -i
CMakeModules/FindQtMmlQt4.cmak
%build
mkdir -p build && pushd build
-export CXXFLAGS="-DF2C_INTEGER=int -DF2C_LOGICAL=long %{optflags}
%{__global_ldflags} -DCOPASI_OVERWRITE_USE_LAPACK -DNO_BLAS_WRAP"
-
-%ifarch %{openblas_arches}
-export LIBBLAS=libopenblas.so
-export INCBLAS=%{_includedir}/openblas
-%else
-export LIBBLAS=libblas.so
-export LIBLAPACK=liblapack.so
-export INCBLAS=%{_includedir}
-%endif
-
+export CXXFLAGS="-I$PWD/../copasi/lapack -DF2C_INTEGER=int -DF2C_LOGICAL=long
%{optflags} %{__global_ldflags}"
%cmake -Wno-dev \
-DCOPASI_OVERRIDE_VERSION:STRING=%{version} \
%if 0%{?with_python3}
@@ -342,14 +323,17 @@ export INCBLAS=%{_includedir}
-DQWT_VERSION_STRING:STRING="%(pkg-config --modversion Qt5Qwt6)" \
-DQWT_LIBRARY:FILEPATH=%{_qt5_libdir}/libqwt-qt5.so \
-DQWT_INCLUDE_DIR:PATH=%{_qt5_headerdir}/qwt \
- -DBUILD_GUI:BOOL=ON -DBUILD_COPASISBW:BOOL=ON --DENABLE_MML:BOOL=ON
-DENABLE_USE_SBMLUNIT=ON \
+ -DBUILD_GUI:BOOL=ON -DBUILD_COPASISBW:BOOL=ON -DENABLE_MML:BOOL=ON
-DENABLE_USE_SBMLUNIT=ON \
-DCMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING="%{__global_ldflags} -pthread" \
-DCMAKE_EXE_LINKER_FLAGS:STRING="%{__global_ldflags}" \
-DMML_INCLUDE_DIR:PATH=%{_qt5_headerdir}/libmml-qt5
-DMML_LIBRARY:FILEPATH=%{_qt5_libdir}/libmml.so \
-DENABLE_SBW_INTEGRATION=ON -DBUILD_CXX_EXAMPLES=OFF \
-DENABLE_COPASI_BANDED_GRAPH:BOOL=ON -DENABLE_COPASI_SEDML:BOOL=ON \
-DENABLE_COPASI_NONLIN_DYN_OSCILLATION:BOOL=ON -DENABLE_COPASI_EXTUNIT:BOOL=ON \
- -DBLAS_blas_LIBRARY:FILEPATH=%{_libdir}/$LIBBLAS
-DLAPACK_lapack_LIBRARY:FILEPATH=%{_libdir}/$LIBLAPACK -DCLAPACK_INCLUDE_DIR:PATH=$INCBLAS
\
+ -DBLAS_blas_LIBRARY:FILEPATH=%{_libdir}/libopenblas.so
-DBLAS_INCLUDE_DIR:PATH=%{_includedir}/openblas \
+ -DCLAPACK_INCLUDE_DIR:PATH= -DLAPACK_lapack_LIBRARY:FILEPATH=%{_libdir}/liblapack.so
-DCLAPACK_LIBRARIES:FILEPATH= \
+ -DCOPASI_OVERWRITE_USE_LAPACK:BOOL=ON -DNO_BLAS_WRAP:BOOL=ON -DBLA_VENDOR=Generic \
+ -DCROSSGUID_INCLUDE_DIR:PATH=%{_includedir}/crossguid2 \
-DENABLE_FLEX_BISON:BOOL=ON -DENABLE_COPASI_PARAMETERFITTING_RESIDUAL_SCALING:BOOL=ON \
-DENABLE_WITH_MERGEMODEL:BOOL=ON -DENABLE_USE_MATH_CONTAINER:BOOL=ON \
-DLIBSBML_INCLUDE_DIR:PATH=%{_includedir}/sbml -DLIBSBML_SHARED:BOOL=ON
-DLIBSBML_LIBRARY:FILEPATH=%{_libdir}/libsbml.so \
@@ -470,6 +454,11 @@ appstream-util validate-relax --nonet
$RPM_BUILD_ROOT%{_metainfodir}/*.appdata.x
%{_datadir}/copasi/doc/
%changelog
+* Sat Mar 16 2019 Antonio Trande <sagitterATfedoraproject.org> - 4.25.207-1
+- Release 4.25 build-207
+- Use openblas always
+- Add crossguid dependency
+
* Fri Mar 08 2019 Antonio Trande <sagitter(a)fedoraproject.org> - 4.24.197-8
- Obsolete COPASI-sharp on fedora 30+/pp64* (rhbz#1588734,#1686738)
diff --git a/sources b/sources
index f6d5ba2..dc418ef 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (COPASI-Build-197.tar.gz) =
273d4144f81bc65af819583141a754bc2e7c50e26bdcf15265045e19434740d84a5ce8ac09aab393658ff20da48f7a487acb7fd58aebdf483df3b40917b3ef30
+SHA512 (COPASI-Build-207.tar.gz) =
eda3c4416912f73849b701c60accf4a1f49317623ba23fea3d4dc6a437b2417a91ae71b9bafa448b57d3ce0e1928b078593b75acdd9bc8ddc9d3973683130603