diff --git a/.gitignore b/.gitignore deleted file mode 100644 index a289a43..0000000 --- a/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -/seqan-src-1.4.1.tar.gz -/seqan-src-1.4.2.tar.gz -/seqan-seqan-v2.0.0-rc1.tar.gz -/seqan-seqan-v2.0.0.tar.gz diff --git a/dead.package b/dead.package new file mode 100644 index 0000000..f4b2d4b --- /dev/null +++ b/dead.package @@ -0,0 +1 @@ +No longer needed in Fedora; deprecated by seqan3 diff --git a/seqan-docpath.patch b/seqan-docpath.patch deleted file mode 100644 index 227307b..0000000 --- a/seqan-docpath.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- util/cmake/SeqAnBuildSystem-orig.cmake 2013-11-20 10:46:58.000000000 +0100 -+++ util/cmake/SeqAnBuildSystem.cmake 2014-06-14 22:28:18.112533516 +0200 -@@ -308,6 +308,7 @@ - else () - set (SEQAN_PREFIX_SHARE "share/${APP_NAME}") - set (SEQAN_PREFIX_SHARE_DOC "share/doc/${APP_NAME}") -+ set (SEQAN_PREFIX_SHARE_DOC "share/doc/seqan/${APP_NAME}") - endif () - endmacro (seqan_setup_install_vars) - - diff --git a/seqan-exclude_bstools_test.patch b/seqan-exclude_bstools_test.patch deleted file mode 100644 index ebf3e85..0000000 --- a/seqan-exclude_bstools_test.patch +++ /dev/null @@ -1,23 +0,0 @@ ---- extras/apps/bs_tools/CMakeLists.orig.txt 2014-10-13 15:03:56.000000000 +0200 -+++ extras/apps/bs_tools/CMakeLists.txt 2014-12-02 11:38:23.759795760 +0100 -@@ -106,7 +106,7 @@ - # ---------------------------------------------------------------------------- - - # (weese:) temporarily disabled app test --seqan_add_app_test (bs_tools) -+# seqan_add_app_test (bs_tools) - - # ---------------------------------------------------------------------------- - # CPack Install ---- core/apps/samcat/CMakeLists.txt 2015-05-15 16:50:20.223867704 +0200 -+++ core/apps/samcat/CMakeLists.orig.txt 2014-10-13 15:03:56.000000000 +0200 -@@ -63,7 +63,7 @@ - # App Test - # ---------------------------------------------------------------------------- - --seqan_add_app_test (samcat) -+#seqan_add_app_test (samcat) - - # ---------------------------------------------------------------------------- - # Setup Common Tool Description for Generic Workflow Nodes - diff --git a/seqan-exclude_splazers_fiona_tests.patch b/seqan-exclude_splazers_fiona_tests.patch deleted file mode 100644 index 9de6a5c..0000000 --- a/seqan-exclude_splazers_fiona_tests.patch +++ /dev/null @@ -1,23 +0,0 @@ ---- core/apps/splazers/CMakeLists.orig.txt 2014-10-13 15:03:56.000000000 +0200 -+++ core/apps/splazers/CMakeLists.txt 2014-11-25 10:41:12.804941092 +0100 -@@ -71,7 +71,7 @@ - # App Test - # ---------------------------------------------------------------------------- - --seqan_add_app_test (splazers) -+# seqan_add_app_test (splazers) - - # ---------------------------------------------------------------------------- - # CPack Install ---- core/apps/fiona/CMakeLists.orig.txt 2014-10-13 15:03:56.000000000 +0200 -+++ core/apps/fiona/CMakeLists.txt 2014-11-25 10:45:11.870330056 +0100 -@@ -79,7 +79,7 @@ - # App Test - # ---------------------------------------------------------------------------- - --seqan_add_app_test (fiona) -+# seqan_add_app_test (fiona) - - # ---------------------------------------------------------------------------- - # Setup Common Tool Description for Generic Workflow Nodes - diff --git a/seqan.spec b/seqan.spec deleted file mode 100644 index a0fa6fb..0000000 --- a/seqan.spec +++ /dev/null @@ -1,286 +0,0 @@ -Name: seqan -Summary: Open source C++ library of efficient algorithms and data structures -Version: 1.4.2 -Release: 37%{?dist} -License: BSD and GPLv3+ and LGPLv3+ -URL: http://www.seqan.de/ -Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz - -## This patch sets a seqan directory for documentation files -Patch0: %{name}-docpath.patch - -## These patches exclude tests of splazers, fiona, bs_tools -## They fail beacause unknown reasons -Patch1: %{name}-exclude_splazers_fiona_tests.patch -Patch2: %{name}-exclude_bstools_test.patch - -BuildRequires: gcc, gcc-c++ -BuildRequires: qt4-devel >= 4.7 -BuildRequires: cmake >= 2.8 -BuildRequires: llvm-devel -BuildRequires: bzip2-devel -BuildRequires: zlib-devel -BuildRequires: boost-devel -BuildRequires: coin-or-lemon-devel -BuildRequires: libstdc++-static -BuildRequires: java-1.8.0-openjdk-devel -## Test -BuildRequires: python2-devel -BuildRequires: python2-nose -BuildRequires: python2-pytest -BuildRequires: python2-jinja2 - -Requires: gawk - -## Bundled files exception https://fedorahosted.org/fpc/ticket/174 -Provides: bundled(gnulib) - -%description -SeqAn is an open source C++ library of efficient algorithms and data structures -for the analysis of sequences with the focus on biological data. -Our library applies a unique generic design that guarantees high performance, -generality, extensibility, and integration with other libraries. - -%package devel -Summary: SeqAn development files - -%description devel -Developer files for SeqAn, in the form for C header files. - -%package doc -Summary: SeqAn documentation -BuildArch: noarch - -%description doc -Info files of SeqAn's apps. - -%prep -%setup -q -n seqan-%{version} -%patch0 -p0 -%patch1 -p0 - -%ifarch %{arm} aarch64 %{power64} s390x -%patch2 -p0 -%endif - -## Remove spurious executable permissions -for i in `find . -perm /111 -type f \( -name "*.h" -o -name "*.cpp" \)`; do -chmod a-x $i -done - -## Renamed each single license file -cp -p extras/apps/rep_sep/LICENSE LGPLv3+.txt -cp -p core/apps/rabema/LICENSE GPLv3+.txt -cp -p LICENSE BSD.txt - -## Make install needs this README file -cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README - -%build -mkdir -p build/Release && pushd build/Release -##This error comes out on >=F22 -##cc1plus: out of memory -%ifarch %{arm} || ( 0%{?fedora} >= 22 ) -SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g') -SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC -Wl,-z,now" -%else -SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS -fPIC -Wl,-z,now" -%endif -export CXXFLAGS="$SEQAN_OPT_FLAGS" -export LDFLAGS="$RPM_LD_FLAGS -fPIC -Wl,-z,now" -cmake \ - -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS" \ - -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ - -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \ - -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \ - -DBUILD_SHARED_LIBS:BOOL=OFF \ - -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \ - -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \ - -DCMAKE_BUILD_TYPE:STRING=Release -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS \ - -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_APP_VERSION:STRING=%{version} \ - -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH="-L%{_libdir} -lz" \ - -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH="-L%{_libdir} -lbz2" \ - -DLEMON_INCLUDE_DIR:PATH=%{_includedir} -DLEMON_LIBRARY:FILEPATH="-L%{_libdir} -lemon" \ - -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python2} \ - -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE ../.. - -##Compiler fails with parallel make -make all - -%install -%make_install -C build/Release INSTALL="install -p" - -## Put header files in ad-hoc include directory -mkdir -p %{buildroot}%{_includedir}/seqan -cp -pr extras/include/seqan/* %{buildroot}%{_includedir}/seqan -cp -pr core/include/seqan/* %{buildroot}%{_includedir}/seqan - -mkdir -p seqandoc -cp -pr %{buildroot}%{_docdir}/seqan/* seqandoc -rm -rf %{buildroot}%{_docdir}/seqan -rm -f seqandoc/*.txt - -## Rename 'join' binary file; it conflicts with the one owned by 'coreutils' package -mv %{buildroot}%{_bindir}/join %{buildroot}%{_bindir}/searchjoin - -## Fix executable permissions -for i in `find %{buildroot}%{_bindir} -perm /644 -type f \( -name "*.sh" \)`; do -chmod a+x $i -done - -%check -pushd build/Release -# Skip 10 - app_test_samcat, 16 - app_test_bs_tools, 20 - app_test_ngs_roi -%ifarch %{arm} aarch64 %{power64} s390x -ctest -I 1,9 --force-new-ctest-process -VV -j1 -%else -ctest --force-new-ctest-process -VV %{?_smp_mflags} -%endif - -%files -%license BSD.txt GPLv3+.txt LGPLv3+.txt -%doc README.rst -%{_bindir}/* - -%files doc -%license BSD.txt GPLv3+.txt LGPLv3+.txt -%doc seqandoc - -%files devel -%license BSD.txt GPLv3+.txt LGPLv3+.txt -%doc README.rst -%{_includedir}/seqan/ - -%changelog -* Sat Jul 14 2018 Fedora Release Engineering - 1.4.2-37 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild - -* Wed Mar 07 2018 Adam Williamson - 1.4.2-36 -- Rebuild to fix GCC 8 mis-compilation - See https://da.gd/YJVwk ("GCC 8 ABI change on x86_64") - -* Thu Feb 22 2018 Antonio Trande - 1.4.2-35 -- Add gcc-c++ BR - -* Fri Feb 09 2018 Fedora Release Engineering - 1.4.2-34 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild - -* Thu Aug 03 2017 Fedora Release Engineering - 1.4.2-33 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild - -* Sun Jul 30 2017 Florian Weimer - 1.4.2-32 -- Rebuild with binutils fix for ppc64le (#1475636) - -* Thu Jul 27 2017 Fedora Release Engineering - 1.4.2-31 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild - -* Tue Jul 04 2017 Jonathan Wakely - 1.4.2-30 -- Rebuilt for Boost 1.64 - -* Mon May 15 2017 Fedora Release Engineering - 1.4.2-29 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild - -* Sat Feb 11 2017 Fedora Release Engineering - 1.4.2-28 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild - -* Fri Jan 27 2017 Jonathan Wakely - 1.4.2-27 -- Rebuilt for Boost 1.63 - -* Sat Nov 12 2016 Antonio Trande - 1.4.2-26 -- Skip tests on s390 and ppc - -* Sat Nov 12 2016 Antonio Trande - 1.4.2-25 -- Skip failed tests - -* Sat Feb 20 2016 Antonio Trande - 1.4.2-24 -- Fixed compiler/linker flags - -* Thu Feb 04 2016 Fedora Release Engineering - 1.4.2-23 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild - -* Fri Jan 15 2016 Jonathan Wakely - 1.4.2-22 -- Rebuilt for Boost 1.60 - -* Wed Oct 21 2015 Antonio Trande - 1.4.2-21 -- Actived hardened build - -* Tue Oct 13 2015 Antonio Trande - 1.4.2-20 -- Rebuilt for cmake 3.4.0 -- Used %%license - -* Thu Aug 27 2015 Jonathan Wakely - 1.4.2-19 -- Rebuilt for Boost 1.59 - -* Wed Jul 29 2015 Fedora Release Engineering - 1.4.2-18 -- Rebuilt for https://fedoraproject.org/wiki/Changes/F23Boost159 - -* Sat Jul 18 2015 Antonio Trande - 1.4.2-17 -- Parallel make always disabled - -* Sat Jul 18 2015 Antonio Trande - 1.4.2-16 -- Rebuild for Boost upgrade to 1.58.0 - -* Fri Jun 19 2015 Fedora Release Engineering - 1.4.2-15 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild - -* Fri May 15 2015 Antonio Trande - 1.4.2-14 -- Reduce optimization to -O0 (cc1plus error persists) - -* Fri May 15 2015 Antonio Trande - 1.4.2-13 -- SPEC cleanups - -* Fri May 15 2015 Antonio Trande - 1.4.2-12 -- Removed -pipe flag because of cc1plus error on ARMs - -* Thu May 14 2015 Antonio Trande - 1.4.2-11 -- Set job=1 to Make on ARMs aarch64 ppc64 ppc64le - -* Thu May 14 2015 Antonio Trande - 1.4.2-10 -- Downgrading to 1.4.2 -- Excluded s390 s390x arches -- Excluded bstools_test on ARMs aarch64 ppc64 ppc64le - -* Mon Jan 26 2015 Petr Machata - 1.4.2-9 -- Rebuild for boost 1.57.0 - -* Tue Dec 02 2014 Antonio Trande - 1.4.2-8 -- Excluded bs_tools test on ARM - -* Mon Dec 01 2014 Antonio Trande - 1.4.2-7 -- Parallel tests not performed on ARM - -* Mon Dec 01 2014 Antonio Trande - 1.4.2-6 -- DBUILD_SHARED_LIBS boolean disabled -- Test enabled - -* Tue Nov 25 2014 Antonio Trande - 1.4.2-5 -- Parallel make excluded on ARM arch - -* Tue Nov 25 2014 Antonio Trande - 1.4.2-4 -- Tests disabled temporarily - -* Sat Nov 22 2014 Antonio Trande - 1.4.2-3 -- Packaged private libraries -- Performed tests -- Splazers and fiona tests excluded - -* Sat Nov 22 2014 Antonio Trande - 1.4.2-2 -- Parallel make excluded on ARM arch - -* Fri Nov 21 2014 Antonio Trande - 1.4.2-1 -- Update to 1.4.2 -- Fixed cmake compiler flags -- Fixed declaration of multiple license -- A doc sub-package is now built - -* Mon Aug 18 2014 Fedora Release Engineering - 1.4.1-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild - -* Sat Jun 14 2014 Antonio Trande 1.4.1-2 -- Added 'Provides:bundled(gnulib)' -- Changed find command for executable permissions fixing -- Use %%make_install -- Fixed wrong-file-end-of-line-encoding warnings - -* Wed Jun 11 2014 Antonio Trande 1.4.1-1 -- First package diff --git a/sources b/sources deleted file mode 100644 index ead6724..0000000 --- a/sources +++ /dev/null @@ -1 +0,0 @@ -e7d2c6cf6474b5186c27ec31bd32738a seqan-src-1.4.2.tar.gz