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=c40a212f7cd....
Change:
+%ifarch %{openblas_arches}
Thanks.
Full change:
============
commit c40a212f7cd7ba9ab741ac7ca4ffb7e18c8be7af
Author: sagitter <sagitter(a)fedoraproject.org>
Date: Sat Nov 18 16:22:12 2017 +0100
Update to version 4.22 -build 170
diff --git a/.gitignore b/.gitignore
index 080be00..9583b19 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,3 +20,4 @@
/COPASI-Build-159.tar.gz
/COPASI-Build-165.tar.gz
/COPASI-Build-166.tar.gz
+/COPASI-Build-170.tar.gz
diff --git a/COPASI-find_QWT5-QTMML-SBW.patch b/COPASI-find_QWT5-QTMML-SBW.patch
index 3cd8d1e..363993a 100644
--- a/COPASI-find_QWT5-QTMML-SBW.patch
+++ b/COPASI-find_QWT5-QTMML-SBW.patch
@@ -1,47 +1,23 @@
--- CMakeModules/FindQwtQt4.orig.cmake 2015-06-17 07:55:18.000000000 +0200
+++ CMakeModules/FindQwtQt4.cmake 2015-06-22 11:34:42.750303512 +0200
-@@ -11,36 +11,18 @@
- # QWT_LIBRARY - Link these to use qwt
-
- find_path(QWT_INCLUDE_DIR qwt.h
-- PATHS $ENV{QWT_DIR}/include
-- $ENV{QWT_DIR}
-- ~/Library/Frameworks
-- /Library/Frameworks
-- /sw/include # Fink
-- /opt/local/include # MacPorts
-- /opt/csw/include # Blastwave
-- /opt/include
+@@ -24,7 +24,7 @@
+ /opt/local/include # MacPorts
+ /opt/csw/include # Blastwave
+ /opt/include
- /usr/freeware/include
-- PATH_SUFFIXES qwt qwt-qt4
-+ PATHS /usr/include
-+ PATH_SUFFIXES qwt5-qt4 qwt
++ /usr/include
+ PATH_SUFFIXES qwt qwt-qt4 qwt-qt5 qwt6
NO_DEFAULT_PATH)
- if (NOT QWT_INCLUDE_DIR)
- find_path(QWT_INCLUDE_DIR qwt.h
-- PATH_SUFFIXES qwt qwt-qt4)
-+ PATH_SUFFIXES qwt5-qt4 qwt)
- endif ()
+@@ -35,7 +35,7 @@
find_library(QWT_LIBRARY
-- NAMES qwt-static
+ NAMES qwt-static
- qwt-qt4
-- qwt
-- PATHS $ENV{QWT_DIR}/lib
-- $ENV{QWT_DIR}
-- ~/Library/Frameworks
-- /Library/Frameworks
-- /sw/lib # Fink
-- /opt/local/lib # MacPorts
-- /opt/csw/lib # Blastwave
-- /opt/lib
-- /usr/freeware/lib64
-+ NAMES qwt5-qt4 qwt
-+ PATHS @@libdir@@
- NO_DEFAULT_PATH)
-
- if (NOT QWT_LIBRARY)
++ qwt5-qt4
+ qwt-qt5
+ qwt
+ PATHS $ENV{QWT_DIR}/lib
--- CMakeModules/FindQtMmlQt4.orig.cmake 2015-06-17 07:55:18.000000000 +0200
+++ CMakeModules/FindQtMmlQt4.cmake 2015-06-22 20:53:18.388194667 +0200
@@ -20,6 +20,7 @@
@@ -98,3 +74,4 @@
$ENV{SBW_DIR}
~/Library/Frameworks
+
diff --git a/COPASI-set_QWTPLOT3D_QT5.patch b/COPASI-set_QWTPLOT3D_QT5.patch
new file mode 100644
index 0000000..87797d0
--- /dev/null
+++ b/COPASI-set_QWTPLOT3D_QT5.patch
@@ -0,0 +1,43 @@
+--- CMakeModules/FindQwtplot3dQt4.orig.cmake 2015-06-17 07:55:18.000000000 +0200
++++ CMakeModules/FindQwtplot3dQt4.cmake 2015-06-23 18:16:42.954635914 +0200
+@@ -10,7 +10,7 @@
+ # QWTPLOT3D_INCLUDE_DIR - the qwtplot3d include directory
+ # QWTPLOT3D_LIBRARY - Link these to use qwtplot3d
+
+-find_path(QWTPLOT3D_INCLUDE_DIR qwt3d_plot.h
++find_path(QWTPLOT3D_INCLUDE_DIR qwt3d_plot3d.h
+ PATHS $ENV{QWTPLOT3D_DIR}/include
+ $ENV{QWTPLOT3D_DIR}
+ ~/Library/Frameworks
+@@ -20,18 +20,17 @@
+ /opt/csw/include # Blastwave
+ /opt/include
+ /usr/freeware/include
+- PATH_SUFFIXES qwtplot3d qwtplot3d-qt4
++ @@qtplot3d_includedir@@
++ PATH_SUFFIXES qwtplot3d-qt5
+ NO_DEFAULT_PATH)
+
+ if (NOT QWTPLOT3D_INCLUDE_DIR)
+ find_path(QWTPLOT3D_INCLUDE_DIR qwt3d_plot.h
+- PATH_SUFFIXES qwtplot3d qwtplot3d-qt4)
++ PATH_SUFFIXES qwtplot3d-qt5)
+ endif (NOT QWTPLOT3D_INCLUDE_DIR)
+
+ find_library(QWTPLOT3D_LIBRARY
+- NAMES qwtplot3d-static
+- qwtplot3d-qt4
+- qwtplot3d
++ NAMES qwtplot3d-qt5
+ PATHS $ENV{QWTPLOT3D_DIR}/lib
+ $ENV{QWTPLOT3D_DIR}
+ ~/Library/Frameworks
+@@ -43,6 +42,7 @@
+ /opt/csw/lib # Blastwave
+ /opt/lib
+ /usr/freeware/lib64
++ @@qtplot3d_libdir@@
+ NO_DEFAULT_PATH)
+
+ if (NOT QWTPLOT3D_LIBRARY)
+
diff --git a/COPASI.spec b/COPASI.spec
index 269497f..6891de9 100644
--- a/COPASI.spec
+++ b/COPASI.spec
@@ -9,7 +9,7 @@
%endif
%endif
-%global buildid 166
+%global buildid 170
%global with_python2 1
%global with_python3 1
@@ -36,7 +36,12 @@
%endif
##Use QWT6? (Experimental)
-%global with_qwt6 1
+%global with_qwt6 0
+
+%global with_qt4 1
+
+# Not ready
+%global with_qt5 0
%global octpkg COPASI
%if 0%{?with_octave}
@@ -47,10 +52,20 @@
%global _docdir_fmt %{name}
+# openblas available on these architectures.
+%if 0%{?fedora} && 0%{?fedora} > 26
+%{!?openblas_arches:%global openblas_arches x86_64 %{ix86} armv7hl %{power64} aarch64
s390x}
+%else
+%{!?openblas_arches:%global openblas_arches x86_64 %{ix86} armv7hl %{power64} aarch64}
+%endif
+%if 0%{?rhel}
+%{!?openblas_arches:%global openblas_arches x86_64 %{ix86} armv7hl %{power64} aarch64}
+%endif
+
Name: COPASI
Summary: Biochemical network simulator
-Version: 4.21.%{buildid}
-Release: 2%{?dist}
+Version: 4.22.%{buildid}
+Release: 1%{?dist}
##Artistic 2.0 is main license
##GPLv2+ is related to a Mixed Source Licensing Scenario
@@ -67,13 +82,20 @@ Source1: %{name}.appdata.xml
%if 0%{?with_qwt6}
BuildRequires: qwt-devel
-%else
+%endif
+%if 0%{?with_qt4}
BuildRequires: qwt5-qt4-devel
+BuildRequires: qwtplot3d-qt4-devel
+BuildRequires: qt-devel
+BuildRequires: qt-webkit-devel
+%endif
+%if 0%{?with_qt5}
+BuildRequires: qwt-qt5-devel
+BuildRequires: qwtplot3d-qt5-devel
+BuildRequires: qt5-qtbase-devel
+BuildRequires: qt5-qtwebkit-devel
%endif
BuildRequires: freeglut-devel
-BuildRequires: qwtplot3d-qt4-devel
-BuildRequires: qt-devel
-BuildRequires: qt-webkit-devel
BuildRequires: libkdeedu-static
BuildRequires: libsbml-devel
BuildRequires: libsedml-devel >= 1:0.4.3-3
@@ -85,8 +107,12 @@ BuildRequires: mesa-libGLU-devel
BuildRequires: cppunit-devel
BuildRequires: libcurl-devel
BuildRequires: libxslt-devel
-BuildRequires: lapack-devel
+%ifarch %{openblas_arches}
+BuildRequires: openblas-devel, openblas-srpm-macros
+%else
BuildRequires: blas-devel
+BuildRequires: lapack-devel
+%endif
BuildRequires: desktop-file-utils
BuildRequires: swig
BuildRequires: expat-devel
@@ -115,6 +141,9 @@ Patch2: %{name}-set_QWTPLOT3D_QT4.patch
##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
+Patch5: %{name}-set_QWTPLOT3D_QT5.patch
+
%description
COPASI is a software application for simulation and analysis of biochemical
networks and their dynamics.
@@ -252,9 +281,10 @@ done
## Strip all .png files
## 'iCCP: known incorrect sRGB profile' warnings
-find . -type f -name "*.png" -exec convert {} -strip {} \;
+#find . -type f -name "*.png" -exec convert {} -strip {} \;
%patch0 -p0
+%patch4 -p0
%if 0%{?with_qwt6}
%patch3 -p0
@@ -269,18 +299,31 @@ sed -e 's|@@libdir@@|%{_libdir}|g' -i
CMakeModules/FindQwtQt4.cmake
sed -e 's|@@_kde4_includedir@@|%{_kde4_includedir}/libkdeedu/qtmml|g' -i
CMakeModules/FindQtMmlQt4.cmake
sed -e 's|@@_kde4_libdir@@|%{_kde4_libdir}|g' -i CMakeModules/FindQtMmlQt4.cmake
-####Set QTPLOT3D-QT4 paths
-%if 0%{?with_qwt6}
+####Set QTPLOT3D-QT* paths
+%if 0%{?with_qt4}
%patch2 -p0
sed -e 's|@@qtplot3d_includedir@@|%{_includedir}|g' -i
CMakeModules/FindQwtplot3dQt4.cmake
sed -e 's|@@qtplot3d_libdir@@|%{_libdir}|g' -i
CMakeModules/FindQwtplot3dQt4.cmake
%endif
-
-%patch4 -p0
+%if 0%{?with_qt5}
+%patch5 -p0
+sed -e 's|@@qtplot3d_includedir@@|%{_qt5_headerdir}|g' -i
CMakeModules/FindQwtplot3dQt4.cmake
+sed -e 's|@@qtplot3d_libdir@@|%{_qt5_libdir}|g' -i
CMakeModules/FindQwtplot3dQt4.cmake
+%endif
%build
mkdir -p build && pushd build
export CXXFLAGS="-DF2C_INTEGER=int -DF2C_LOGICAL=long %{optflags} -Wl,-z,relro -fPIC
-pie -Wl,-z,now -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
+
%cmake -Wno-dev \
-DCOPASI_OVERRIDE_VERSION:STRING=%{version} \
%if 0%{?with_python2}
@@ -313,7 +356,19 @@ export CXXFLAGS="-DF2C_INTEGER=int -DF2C_LOGICAL=long
%{optflags} -Wl,-z,relro -
%endif
-DCSHARP_COMPILER:FILEPATH=%{_bindir}/mcs \
%if 0%{?with_qwt6}
- -DEXTRA_MOC_OPTIONS="-DQWT_VERSION=0x60102" \
+ -DQWT_VERSION_STRING:STRING=6.1.3 \
+%endif
+%if 0%{?with_qt4}
+ -DQT_QMAKE_EXECUTABLE:FILEPATH=%{_bindir}/qmake-qt4 \
+ -DQWT_VERSION_STRING:STRING=5.2.2 \
+ -DQWT_LIBRARY:FILEPATH=%{_qt4_libdir}/libqwt5-qt4.so \
+ -DQWT_INCLUDE_DIR:PATH=%{_qt4_headerdir}/qwt5-qt4 \
+%endif
+%if 0%{?with_qt5}
+ -DQT_QMAKE_EXECUTABLE:FILEPATH=%{_bindir}/qmake-qt5 \
+ -DQWT_VERSION_STRING:STRING=6.1.3 \
+ -DQWT_LIBRARY:FILEPATH=%{_qt5_libdir}/libqwt-qt5.so \
+ -DQWT_INCLUDE_DIR:PATH=%{_qt5_headerdir}/qwt \
%endif
-DBUILD_GUI:BOOL=ON -DBUILD_COPASISBW:BOOL=ON --DENABLE_MML:BOOL=ON
-DENABLE_USE_SBMLUNIT=ON \
-DCMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING="%{__global_ldflags} -Wl,-z,relro -fPIC
-pie -Wl,-z,now -pthread" \
@@ -322,7 +377,7 @@ export CXXFLAGS="-DF2C_INTEGER=int -DF2C_LOGICAL=long %{optflags}
-Wl,-z,relro -
-DENABLE_SBW_INTEGRATION=ON -DBUILD_CXX_EXAMPLES=ON \
-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.so \
+ -DBLAS_blas_LIBRARY:FILEPATH=%{_libdir}/$LIBBLAS
-DLAPACK_lapack_LIBRARY:FILEPATH=%{_libdir}/$LIBLAPACK -DCLAPACK_INCLUDE_DIR:PATH=$INCBLAS
\
-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 -DF2C_INCLUDE_DIR:PATH=%{_includedir} \
@@ -344,6 +399,16 @@ popd
%if 0%{?with_python3}
mkdir -p build2 && pushd build2
export CXXFLAGS="-DF2C_INTEGER=int -DF2C_LOGICAL=long %{optflags} -Wl,-z,relro -fPIC
-pie -Wl,-z,now -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
+
%cmake -Wno-dev \
-DCOPASI_OVERRIDE_VERSION:STRING=%{version} \
-DENABLE_PYTHON:BOOL=ON \
@@ -379,7 +444,7 @@ export CXXFLAGS="-DF2C_INTEGER=int -DF2C_LOGICAL=long %{optflags}
-Wl,-z,relro -
-DENABLE_SBW_INTEGRATION=ON -DBUILD_CXX_EXAMPLES=ON \
-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.so \
+ -DBLAS_blas_LIBRARY:FILEPATH=%{_libdir}/$LIBBLAS
-DLAPACK_lapack_LIBRARY:FILEPATH=%{_libdir}/$LIBLAPACK -DCLAPACK_INCLUDE_DIR:PATH=$INCBLAS
\
-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 -DF2C_INCLUDE_DIR:PATH=%{_includedir} \
@@ -552,6 +617,10 @@ appstream-util validate-relax --nonet
$RPM_BUILD_ROOT%{_datadir}/appdata/*.appda
%{_datadir}/copasi/doc/
%changelog
+* Sat Nov 11 2017 Antonio Trande <sagitterATfedoraproject.org> - 4.22.170-1
+- Update to version 4.22 -build 170
+- Use OpenBlas
+
* Thu Oct 12 2017 Antonio Trande <sagitterATfedoraproject.org> - 4.21.166-2
- Remove old Obsoletes
diff --git a/sources b/sources
index 8ab5443..225b2d0 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (COPASI-Build-166.tar.gz) =
4b54fddcf02985c2dd9387c8a3e99479bd31be403f2f2b691151da5ea8f3eaa42b0723ac92b32259bee6e220c94a8693fb4892de9b5a281b90b02dbb0fb45bcf
+SHA512 (COPASI-Build-170.tar.gz) =
086d8cf4178e55b260787e9c02c9c253edfd07878b5c67f6d757f87bb0f26dadaeb2fdf7c61093eb2f7dab1894525217bec8e91cf06ce725b1958cce350f414d