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| 76ccc8ff92 | |||
| 87daad9e2d |
7 changed files with 1 additions and 381 deletions
4
.gitignore
vendored
4
.gitignore
vendored
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@ -1,4 +0,0 @@
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/seqan-src-1.4.1.tar.gz
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/seqan-src-1.4.2.tar.gz
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/seqan-seqan-v2.0.0-rc1.tar.gz
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/seqan-seqan-v2.0.0.tar.gz
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1
dead.package
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1
dead.package
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@ -0,0 +1 @@
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No longer needed in Fedora; deprecated by seqan3
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@ -1,11 +0,0 @@
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--- util/cmake/SeqAnBuildSystem-orig.cmake 2013-11-20 10:46:58.000000000 +0100
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+++ util/cmake/SeqAnBuildSystem.cmake 2014-06-14 22:28:18.112533516 +0200
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@@ -308,6 +308,7 @@
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else ()
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set (SEQAN_PREFIX_SHARE "share/${APP_NAME}")
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set (SEQAN_PREFIX_SHARE_DOC "share/doc/${APP_NAME}")
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+ set (SEQAN_PREFIX_SHARE_DOC "share/doc/seqan/${APP_NAME}")
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endif ()
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endmacro (seqan_setup_install_vars)
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@ -1,23 +0,0 @@
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--- extras/apps/bs_tools/CMakeLists.orig.txt 2014-10-13 15:03:56.000000000 +0200
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+++ extras/apps/bs_tools/CMakeLists.txt 2014-12-02 11:38:23.759795760 +0100
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@@ -106,7 +106,7 @@
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# ----------------------------------------------------------------------------
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# (weese:) temporarily disabled app test
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-seqan_add_app_test (bs_tools)
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+# seqan_add_app_test (bs_tools)
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# ----------------------------------------------------------------------------
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# CPack Install
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--- core/apps/samcat/CMakeLists.txt 2015-05-15 16:50:20.223867704 +0200
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+++ core/apps/samcat/CMakeLists.orig.txt 2014-10-13 15:03:56.000000000 +0200
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@@ -63,7 +63,7 @@
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# App Test
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# ----------------------------------------------------------------------------
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-seqan_add_app_test (samcat)
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+#seqan_add_app_test (samcat)
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# ----------------------------------------------------------------------------
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# Setup Common Tool Description for Generic Workflow Nodes
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@ -1,23 +0,0 @@
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--- core/apps/splazers/CMakeLists.orig.txt 2014-10-13 15:03:56.000000000 +0200
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+++ core/apps/splazers/CMakeLists.txt 2014-11-25 10:41:12.804941092 +0100
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@@ -71,7 +71,7 @@
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# App Test
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# ----------------------------------------------------------------------------
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-seqan_add_app_test (splazers)
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+# seqan_add_app_test (splazers)
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# ----------------------------------------------------------------------------
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# CPack Install
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--- core/apps/fiona/CMakeLists.orig.txt 2014-10-13 15:03:56.000000000 +0200
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+++ core/apps/fiona/CMakeLists.txt 2014-11-25 10:45:11.870330056 +0100
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@@ -79,7 +79,7 @@
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# App Test
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# ----------------------------------------------------------------------------
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-seqan_add_app_test (fiona)
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+# seqan_add_app_test (fiona)
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# ----------------------------------------------------------------------------
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# Setup Common Tool Description for Generic Workflow Nodes
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319
seqan.spec
319
seqan.spec
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@ -1,319 +0,0 @@
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# LTO flags prevent the linker's work
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# /usr/bin/ld: error: lto-wrapper failed
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%define _lto_cflags %{nil}
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Name: seqan
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Summary: Open source C++ library of efficient algorithms and data structures
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Version: 1.4.2
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Release: 50%{?dist}
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License: BSD and GPLv3+ and LGPLv3+
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URL: http://www.seqan.de/
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Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz
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## This patch sets a seqan directory for documentation files
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Patch0: %{name}-docpath.patch
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## These patches exclude tests of splazers, fiona, bs_tools
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||||||
## They fail beacause unknown reasons
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Patch1: %{name}-exclude_splazers_fiona_tests.patch
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Patch2: %{name}-exclude_bstools_test.patch
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BuildRequires: make
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BuildRequires: gcc, gcc-c++
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BuildRequires: qt4-devel >= 4.7
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BuildRequires: cmake
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BuildRequires: llvm-devel
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BuildRequires: bzip2-devel
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BuildRequires: zlib-devel
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BuildRequires: boost-devel
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BuildRequires: coin-or-lemon-devel
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BuildRequires: libstdc++-static
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%ifarch %{java_arches}
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BuildRequires: java-1.8.0-openjdk-devel
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||||||
%endif
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BuildRequires: python3-devel
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BuildRequires: python3-setuptools
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Requires: gawk
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||||||
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||||||
## Bundled files exception https://fedorahosted.org/fpc/ticket/174
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Provides: bundled(gnulib)
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%description
|
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||||||
SeqAn is an open source C++ library of efficient algorithms and data structures
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for the analysis of sequences with the focus on biological data.
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||||||
Our library applies a unique generic design that guarantees high performance,
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|
||||||
generality, extensibility, and integration with other libraries.
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|
||||||
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|
||||||
%package devel
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||||||
Summary: SeqAn development files
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|
||||||
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||||||
%description devel
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||||||
Developer files for SeqAn, in the form for C header files.
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|
||||||
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||||||
%package doc
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|
||||||
Summary: SeqAn documentation
|
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||||||
BuildArch: noarch
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|
||||||
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|
||||||
%description doc
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|
||||||
Info files of SeqAn's apps.
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|
||||||
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||||||
%prep
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|
||||||
%setup -q -n seqan-%{version}
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|
||||||
%patch0 -p0
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|
||||||
%patch1 -p0
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|
||||||
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|
||||||
%ifarch %{arm} aarch64 %{power64} s390x
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|
||||||
%patch2 -p0
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|
||||||
%endif
|
|
||||||
|
|
||||||
## Remove spurious executable permissions
|
|
||||||
find . -type f -name "*.h" -exec chmod 0644 '{}' \;
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|
||||||
find . -type f -name "*.cpp" -exec chmod 0644 '{}' \;
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|
||||||
|
|
||||||
## Renamed each single license file
|
|
||||||
cp -p extras/apps/rep_sep/LICENSE LGPLv3+.txt
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|
||||||
cp -p core/apps/rabema/LICENSE GPLv3+.txt
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|
||||||
cp -p LICENSE BSD.txt
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|
||||||
|
|
||||||
## Make install needs this README file
|
|
||||||
cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README
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|
||||||
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|
||||||
%build
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|
||||||
mkdir -p build/Release && pushd build/Release
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||||||
# cc1plus: out of memory on ARM
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||||||
%ifarch %{arm}
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|
||||||
SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g' -e 's/-Wp,-D_FORTIFY_SOURCE=2//g')
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SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC"
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||||||
%else
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||||||
SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS -fPIC"
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||||||
%endif
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||||||
export CXXFLAGS="-std=c++14 $SEQAN_OPT_FLAGS -lemon"
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||||||
export LDFLAGS="$RPM_LD_FLAGS -fPIC"
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cmake \
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||||||
-DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS" \
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||||||
-DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \
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||||||
-DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \
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||||||
-DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \
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|
||||||
-DBUILD_SHARED_LIBS:BOOL=OFF \
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|
||||||
-DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \
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|
||||||
-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
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|
||||||
-DCMAKE_BUILD_TYPE:STRING=Release -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS \
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|
||||||
-DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_APP_VERSION:STRING=%{version} \
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|
||||||
-DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH="-L%{_libdir} -lz" \
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|
||||||
-DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH="-L%{_libdir} -lbz2" \
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|
||||||
-DLEMON_INCLUDE_DIR:PATH=%{_includedir} -DLEMON_LIBRARY:FILEPATH="-L%{_libdir} -lemon" \
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|
||||||
-DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \
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|
||||||
-DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE ../..
|
|
||||||
|
|
||||||
## Compiler fails with parallel make
|
|
||||||
make -j1 all
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|
||||||
|
|
||||||
%install
|
|
||||||
%make_install -C build/Release
|
|
||||||
|
|
||||||
## Put header files in ad-hoc include directory
|
|
||||||
mkdir -p %{buildroot}%{_includedir}/seqan
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|
||||||
cp -pr extras/include/seqan/* %{buildroot}%{_includedir}/seqan
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|
||||||
cp -pr core/include/seqan/* %{buildroot}%{_includedir}/seqan
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|
||||||
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|
||||||
mkdir -p seqandoc
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|
||||||
cp -pr %{buildroot}%{_docdir}/seqan/* seqandoc
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|
||||||
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
|
|
||||||
find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \;
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|
||||||
|
|
||||||
%files
|
|
||||||
%license BSD.txt GPLv3+.txt LGPLv3+.txt
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|
||||||
%doc README.rst
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|
||||||
%{_bindir}/*
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|
||||||
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|
||||||
%files doc
|
|
||||||
%license BSD.txt GPLv3+.txt LGPLv3+.txt
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|
||||||
%doc seqandoc
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|
||||||
|
|
||||||
%files devel
|
|
||||||
%license BSD.txt GPLv3+.txt LGPLv3+.txt
|
|
||||||
%doc README.rst
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|
||||||
%{_includedir}/seqan/
|
|
||||||
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|
||||||
%changelog
|
|
||||||
* Sat Jul 23 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-50
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|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
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|
||||||
|
|
||||||
* Tue Jul 05 2022 Antonio Trande <sagitter@fedoraproject.org> - 1.4.2-49
|
|
||||||
- Drop JDK in i686 builds
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|
||||||
|
|
||||||
* Sat Feb 05 2022 Jiri Vanek <jvanek@redhat.com> - 1.4.2-48
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|
||||||
- Rebuilt for java-17-openjdk as system jdk
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|
||||||
|
|
||||||
* Sat Jan 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-47
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
|
|
||||||
|
|
||||||
* Fri Jul 23 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-46
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
|
|
||||||
|
|
||||||
* Wed Jan 27 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-45
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
|
|
||||||
|
|
||||||
* Wed Aug 19 2020 Jeff Law <law@redhat.com> - 1.4.2-44
|
|
||||||
- Force C++14 as this code is not C++17 ready
|
|
||||||
|
|
||||||
* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-43
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|
||||||
- Second attempt - Rebuilt for
|
|
||||||
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
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|
||||||
|
|
||||||
* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-42
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
|
|
||||||
|
|
||||||
* Wed Jun 24 2020 Antonio Trande <sagitter@fedoraproject.org> - 1.4.2-41
|
|
||||||
- BuildRequires python3-setuptools
|
|
||||||
|
|
||||||
* Fri Feb 07 2020 Antonio Trande <sagitter@fedoraproject.org> - 1.4.2-40
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
|
|
||||||
- Linker flag to liblemon
|
|
||||||
|
|
||||||
* Fri Aug 02 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-39
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
|
|
||||||
- Do not perform the tests (need Python2 tools)
|
|
||||||
|
|
||||||
* Sat Feb 02 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-38
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
|
|
||||||
|
|
||||||
* Sat Jul 14 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-37
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
|
|
||||||
|
|
||||||
* Wed Mar 07 2018 Adam Williamson <awilliam@redhat.com> - 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 <sagitter@fedoraproject.org> - 1.4.2-35
|
|
||||||
- Add gcc-c++ BR
|
|
||||||
|
|
||||||
* Fri Feb 09 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-34
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
|
|
||||||
|
|
||||||
* Thu Aug 03 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-33
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
|
|
||||||
|
|
||||||
* Sun Jul 30 2017 Florian Weimer <fweimer@redhat.com> - 1.4.2-32
|
|
||||||
- Rebuild with binutils fix for ppc64le (#1475636)
|
|
||||||
|
|
||||||
* Thu Jul 27 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-31
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
|
|
||||||
|
|
||||||
* Tue Jul 04 2017 Jonathan Wakely <jwakely@redhat.com> - 1.4.2-30
|
|
||||||
- Rebuilt for Boost 1.64
|
|
||||||
|
|
||||||
* Mon May 15 2017 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4.2-29
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild
|
|
||||||
|
|
||||||
* Sat Feb 11 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-28
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
|
|
||||||
|
|
||||||
* Fri Jan 27 2017 Jonathan Wakely <jwakely@redhat.com> - 1.4.2-27
|
|
||||||
- Rebuilt for Boost 1.63
|
|
||||||
|
|
||||||
* Sat Nov 12 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-26
|
|
||||||
- Skip tests on s390 and ppc
|
|
||||||
|
|
||||||
* Sat Nov 12 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-25
|
|
||||||
- Skip failed tests
|
|
||||||
|
|
||||||
* Sat Feb 20 2016 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-24
|
|
||||||
- Fixed compiler/linker flags
|
|
||||||
|
|
||||||
* Thu Feb 04 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.4.2-23
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
|
|
||||||
|
|
||||||
* Fri Jan 15 2016 Jonathan Wakely <jwakely@redhat.com> - 1.4.2-22
|
|
||||||
- Rebuilt for Boost 1.60
|
|
||||||
|
|
||||||
* Wed Oct 21 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-21
|
|
||||||
- Actived hardened build
|
|
||||||
|
|
||||||
* Tue Oct 13 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-20
|
|
||||||
- Rebuilt for cmake 3.4.0
|
|
||||||
- Used %%license
|
|
||||||
|
|
||||||
* Thu Aug 27 2015 Jonathan Wakely <jwakely@redhat.com> - 1.4.2-19
|
|
||||||
- Rebuilt for Boost 1.59
|
|
||||||
|
|
||||||
* Wed Jul 29 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4.2-18
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Changes/F23Boost159
|
|
||||||
|
|
||||||
* Sat Jul 18 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-17
|
|
||||||
- Parallel make always disabled
|
|
||||||
|
|
||||||
* Sat Jul 18 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-16
|
|
||||||
- Rebuild for Boost upgrade to 1.58.0
|
|
||||||
|
|
||||||
* Fri Jun 19 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4.2-15
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- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
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* Fri May 15 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-14
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- Reduce optimization to -O0 (cc1plus error persists)
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||||||
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||||||
* Fri May 15 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-13
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- SPEC cleanups
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||||||
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||||||
* Fri May 15 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-12
|
|
||||||
- Removed -pipe flag because of cc1plus error on ARMs
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||||||
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||||||
* Thu May 14 2015 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-11
|
|
||||||
- Set job=1 to Make on ARMs aarch64 ppc64 ppc64le
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||||||
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|
||||||
* Thu May 14 2015 Antonio Trande <sagitterATfedoraproject.org> - 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 <pmachata@redhat.com> - 1.4.2-9
|
|
||||||
- Rebuild for boost 1.57.0
|
|
||||||
|
|
||||||
* Tue Dec 02 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-8
|
|
||||||
- Excluded bs_tools test on ARM
|
|
||||||
|
|
||||||
* Mon Dec 01 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-7
|
|
||||||
- Parallel tests not performed on ARM
|
|
||||||
|
|
||||||
* Mon Dec 01 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-6
|
|
||||||
- DBUILD_SHARED_LIBS boolean disabled
|
|
||||||
- Test enabled
|
|
||||||
|
|
||||||
* Tue Nov 25 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-5
|
|
||||||
- Parallel make excluded on ARM arch
|
|
||||||
|
|
||||||
* Tue Nov 25 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-4
|
|
||||||
- Tests disabled temporarily
|
|
||||||
|
|
||||||
* Sat Nov 22 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-3
|
|
||||||
- Packaged private libraries
|
|
||||||
- Performed tests
|
|
||||||
- Splazers and fiona tests excluded
|
|
||||||
|
|
||||||
* Sat Nov 22 2014 Antonio Trande <sagitterATfedoraproject.org> - 1.4.2-2
|
|
||||||
- Parallel make excluded on ARM arch
|
|
||||||
|
|
||||||
* Fri Nov 21 2014 Antonio Trande <sagitterATfedoraproject.org> - 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 <rel-eng@lists.fedoraproject.org> - 1.4.1-3
|
|
||||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
|
|
||||||
|
|
||||||
* Sat Jun 14 2014 Antonio Trande <sagitterATfedoraproject.org> 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 <sagitterATfedoraproject.org> 1.4.1-1
|
|
||||||
- First package
|
|
||||||
1
sources
1
sources
|
|
@ -1 +0,0 @@
|
||||||
e7d2c6cf6474b5186c27ec31bd32738a seqan-src-1.4.2.tar.gz
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue