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....
Change:
-%ifarch %{ix86} x86_64 sparc sparcv9 ia64 %{arm} aarch64 alpha s390x ppc
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