From d8402e87f8f0dc00d862fe2dc15e2d82289242fe Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 27 Jan 2024 02:35:31 +0000 Subject: [PATCH 1/6] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild --- seqan2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan2.spec b/seqan2.spec index 5078772..953b046 100644 --- a/seqan2.spec +++ b/seqan2.spec @@ -13,7 +13,7 @@ Obsoletes: seqan2-doc < 0:2.4.0-8 Name: seqan2 Summary: C++ library of efficient algorithms and data structures Version: 2.4.0 -Release: 20%{?dist} +Release: 21%{?dist} License: BSD URL: http://www.seqan.de/ Source0: https://github.com/seqan/seqan/archive/seqan-v%{version}.tar.gz#/seqan-seqan-v%{version}.tar.gz @@ -271,6 +271,9 @@ ctest --force-new-ctest-process -VV --parallel %{?_smp_mflags} -E app_test_fiona %endif %changelog +* Sat Jan 27 2024 Fedora Release Engineering - 2.4.0-21 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + * Sat Jul 22 2023 Fedora Release Engineering - 2.4.0-20 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild From 0e48e9628af5463dda0f6c6a519cad9c5acd69e9 Mon Sep 17 00:00:00 2001 From: Jerry James Date: Mon, 29 Jan 2024 20:05:40 -0700 Subject: [PATCH 2/6] Remove unused dependency on coin-or-lemon Other changes: - Convert License fields to SPDX - Stop building for 32-bit x86 - Depend on fontawesome4 for F39+, not fontawesome - The headers subpackage needs bzip2-devel and zlib-devel - Fix a few typos --- seqan2.spec | 47 +++++++++++++++++++++++++++++------------------ 1 file changed, 29 insertions(+), 18 deletions(-) diff --git a/seqan2.spec b/seqan2.spec index 953b046..4b12d7a 100644 --- a/seqan2.spec +++ b/seqan2.spec @@ -1,8 +1,5 @@ %global __cmake_in_source_build 1 -# Default ld_as_needed flag breaks executables linkage -%undefine _ld_as_needed - # Tests need Python2 to be executed %global with_check 0 @@ -13,9 +10,9 @@ Obsoletes: seqan2-doc < 0:2.4.0-8 Name: seqan2 Summary: C++ library of efficient algorithms and data structures Version: 2.4.0 -Release: 21%{?dist} -License: BSD -URL: http://www.seqan.de/ +Release: 22%{?dist} +License: BSD-3-Clause +URL: https://www.seqan.de/ Source0: https://github.com/seqan/seqan/archive/seqan-v%{version}.tar.gz#/seqan-seqan-v%{version}.tar.gz # Disable automatic stripping on no-DEVELOP seqan build systems @@ -27,6 +24,9 @@ Patch1: %{name}-set_config_filepath.patch # Set paths of plot.awk and ps2pswLinks.gawk files Patch2: %{name}-set_awk_installation.patch +# See https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval +ExcludeArch: %{ix86} + BuildRequires: make BuildRequires: qt4-devel BuildRequires: cmake, gcc-c++ @@ -34,7 +34,6 @@ BuildRequires: llvm-devel BuildRequires: bzip2-devel BuildRequires: zlib-devel BuildRequires: boost-devel -BuildRequires: coin-or-lemon-devel BuildRequires: libstdc++-static BuildRequires: python3-devel @@ -67,7 +66,7 @@ As such, it contains algorithms and data structures for %package apps Summary: SeqAn (2.x.x) applications -## Seqan apps are licenses under BSD and GPLv3+ and LGPLv3+. +## Seqan apps are licensed under BSD and GPLv3+ and LGPLv3+. # # BSD (3-clauses): alf, bs_tools, fiona, fx_tools, gustaf # insegt, mason2, ngs_roi, param_chooser, rabema, razers3 @@ -84,7 +83,7 @@ Summary: SeqAn (2.x.x) applications # LGPLv3 gives you permission to relicense the code under GPLv3 # BSD (3-clauses) is compatible with GPLv3 # We can use a collective license: -License: GPLv3+ and BSD and LGPLv3+ +License: GPL-3.0-or-later AND BSD-3-Clause AND LGPL-3.0-or-later Requires: gawk%{?_isa} # 'seqan2' is the most recent version of 'SeqAn' @@ -101,13 +100,15 @@ Summary: SeqAn (2.x.x) headers only files # basic/boost*.h libraries are distributed under Boost # bam_io/bam_index_bai.h is distributed under MIT # Although Boost, zlib, MIT are GPL compatible, they're all tagged anyway -License: GPLv3+ and BSD and MIT and LGPLv3+ and zlib and Boost +License: GPL-3.0-or-later AND BSD-3-Clause AND MIT AND LGPL-3.0-or-later AND Zlib AND BSL-1.0 +Requires: bzip2-devel%{?_isa} +Requires: zlib-devel%{?_isa} Provides: bundled(bzip2stream) Provides: bundled(zipstream) %description headers -C headers files of SeqAn, including pkconfig and CMake configuration files. +C headers files of SeqAn, including pkgconfig and CMake configuration files. %package examples Summary: SeqAn (2.x.x) examples @@ -122,10 +123,14 @@ Summary: SeqAn (2.x.x) documentation # 3L is licensed under MIT # Less and bootstrap files is licensed under ASL 2.0 # jquery-bbq are licensed under LGPLv3+ -License: LGPLv3+ and MIT and ASL 2.0 +License: LGPL-3.0-or-later AND MIT AND Apache-2.0 BuildRequires: python3-sphinx BuildRequires: python3-sphinx_rtd_theme +%if 0%{?fedora} > 38 +Requires: fontawesome4-fonts-web +%else Requires: fontawesome-fonts-web +%endif BuildArch: noarch # https://github.com/mateuszkocz/3l @@ -175,7 +180,6 @@ SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON \ -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH=%{_libdir}/libz.so \ -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH=%{_libdir}/libbz2.so \ - -DLEMON_INCLUDE_DIR:PATH=%{_includedir} -DLEMON_LIBRARY:FILEPATH=%{_libdir}/libemon.so \ -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ -DSPHINX_MAN_OUTPUT:BOOL=ON \ @@ -200,7 +204,6 @@ SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON \ -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH=%{_libdir}/libz.so \ -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH=%{_libdir}/libbz2.so \ - -DLEMON_INCLUDE_DIR:PATH=%{_includedir} -DLEMON_LIBRARY:FILEPATH=%{_libdir}/libemon.so \ -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ -DYARA_LARGE_CONTIGS:BOOL=OFF \ -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ @@ -215,10 +218,10 @@ make -O -j1 # Unbundle font-awesome fonts %if 0%{?with_doc} -ln -s %{_datadir}/font-awesome/scss %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/scss -ln -s %{_datadir}/font-awesome/css %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/css -ln -s %{_datadir}/font-awesome/fonts %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/fonts -ln -s %{_datadir}/font-awesome/less %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/less +ln -s %{_datadir}/font-awesome-web/scss %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/scss +ln -s %{_datadir}/font-awesome-web/css %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/css +ln -s %{_datadir}/fonts/fontawesome %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/fonts +ln -s %{_datadir}/font-awesome-web/less %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/less %endif ## Fix executable permissions @@ -271,6 +274,14 @@ ctest --force-new-ctest-process -VV --parallel %{?_smp_mflags} -E app_test_fiona %endif %changelog +* Mon Jan 29 2024 Jerry James - 2.4.0-22 +- Remove unused dependency on coin-or-lemon +- Convert License fields to SPDX +- Stop building for 32-bit x86 +- Depend on fontawesome4 for F39+, not fontawesome +- The headers subpackage needs bzip2-devel and zlib-devel +- Fix a few typos + * Sat Jan 27 2024 Fedora Release Engineering - 2.4.0-21 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From 5217bd164657c19ead20d2e02cb9afc1282915fa Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Tue, 30 Jan 2024 19:00:11 +0100 Subject: [PATCH 3/6] Change CMake commands --- seqan2.spec | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/seqan2.spec b/seqan2.spec index 4b12d7a..052a24d 100644 --- a/seqan2.spec +++ b/seqan2.spec @@ -1,5 +1,3 @@ -%global __cmake_in_source_build 1 - # Tests need Python2 to be executed %global with_check 0 @@ -93,6 +91,7 @@ Provides: seqan = 0:%{version}-%{release} %description apps All SeqAn applications. + %package headers Summary: SeqAn (2.x.x) headers only files @@ -110,6 +109,7 @@ Provides: bundled(zipstream) %description headers C headers files of SeqAn, including pkgconfig and CMake configuration files. + %package examples Summary: SeqAn (2.x.x) examples Requires: %{name}-apps%{?_isa} = %{version}-%{release} @@ -164,9 +164,9 @@ cp -p apps/rabema/COPYING apps/rabema/rabema-COPYING rm -rf util/py_lib/seqan/dox/tpl/lib/font-awesome/* %build -mkdir -p build/library && pushd build/library +mkdir -p build/library SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -%cmake \ +%cmake -S ./ -B build/library \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ @@ -184,13 +184,13 @@ SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ -DSPHINX_MAN_OUTPUT:BOOL=ON \ -DSPHINX_TEXT_OUTPUT:BOOL=ON \ - -DYARA_LARGE_CONTIGS:BOOL=OFF ../.. + -DYARA_LARGE_CONTIGS:BOOL=OFF %make_build popd -mkdir -p build/Release && pushd build/Release +mkdir -p build/Release SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -%cmake \ +%cmake -S ./ -B build/Release \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ @@ -208,7 +208,7 @@ SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -DYARA_LARGE_CONTIGS:BOOL=OFF \ -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ -DSPHINX_MAN_OUTPUT:BOOL=ON \ - -DSPHINX_TEXT_OUTPUT:BOOL=ON ../.. + -DSPHINX_TEXT_OUTPUT:BOOL=ON # Disable parallel Make jobs to prevent compiler errors make -O -j1 From fe3bf7292c4b6709ce364d0050e3d4860528bd27 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Tue, 30 Jan 2024 19:56:17 +0100 Subject: [PATCH 4/6] Fix CMake commands --- seqan2.spec | 43 ++++--------------------------------------- 1 file changed, 4 insertions(+), 39 deletions(-) diff --git a/seqan2.spec b/seqan2.spec index 052a24d..8ccf6df 100644 --- a/seqan2.spec +++ b/seqan2.spec @@ -63,28 +63,21 @@ As such, it contains algorithms and data structures for %package apps Summary: SeqAn (2.x.x) applications - ## Seqan apps are licensed under BSD and GPLv3+ and LGPLv3+. -# # BSD (3-clauses): alf, bs_tools, fiona, fx_tools, gustaf # insegt, mason2, ngs_roi, param_chooser, rabema, razers3 # sak, sam2matrix, samcat, searchjoin, seqcons2, yara # ngs_roi, pair_align, ngs_roi. -# # GPLv3+: rabema. -# # LGPLv3+: dfi, insegt, micro_razers, pair_align # param_chooser, razers, razers3, rep_sep, sak # seqan_tcoffee, sgip, snp_store, splazers, stellar # tree_recon. -## # LGPLv3 gives you permission to relicense the code under GPLv3 # BSD (3-clauses) is compatible with GPLv3 # We can use a collective license: License: GPL-3.0-or-later AND BSD-3-Clause AND LGPL-3.0-or-later Requires: gawk%{?_isa} - -# 'seqan2' is the most recent version of 'SeqAn' Obsoletes: seqan <= 0:1.4.2 Provides: seqan = 0:%{version}-%{release} @@ -164,33 +157,8 @@ cp -p apps/rabema/COPYING apps/rabema/rabema-COPYING rm -rf util/py_lib/seqan/dox/tpl/lib/font-awesome/* %build -mkdir -p build/library SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -%cmake -S ./ -B build/library \ - -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ - -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ - -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ - -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/%{name} \ - -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 \ - -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_LIBRARY \ - -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON \ - -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH=%{_libdir}/libz.so \ - -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH=%{_libdir}/libbz2.so \ - -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ - -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ - -DSPHINX_MAN_OUTPUT:BOOL=ON \ - -DSPHINX_TEXT_OUTPUT:BOOL=ON \ - -DYARA_LARGE_CONTIGS:BOOL=OFF -%make_build -popd - -mkdir -p build/Release -SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -%cmake -S ./ -B build/Release \ +%cmake -Wno-dev \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ @@ -209,12 +177,10 @@ SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ -DSPHINX_MAN_OUTPUT:BOOL=ON \ -DSPHINX_TEXT_OUTPUT:BOOL=ON -# Disable parallel Make jobs to prevent compiler errors -make -O -j1 +%cmake_build %install -%make_install -C build/library -%make_install -C build/Release +%cmake_install # Unbundle font-awesome fonts %if 0%{?with_doc} @@ -239,8 +205,7 @@ rm -f %{buildroot}%{_datadir}/doc/seqan2/README.rst %if 0%{?with_check} %check -pushd build/Release -ctest --force-new-ctest-process -VV --parallel %{?_smp_mflags} -E app_test_fiona +%ctest -- -E app_test_fiona %endif %files apps From d81a07ca64a8dd478443a99bdaf4d93f4e0967e7 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Tue, 30 Jan 2024 21:03:03 +0100 Subject: [PATCH 5/6] Switch back to old CMake style --- seqan2.spec | 37 +++++++++++++++++++++++++++++++++---- 1 file changed, 33 insertions(+), 4 deletions(-) diff --git a/seqan2.spec b/seqan2.spec index 8ccf6df..1c59c8a 100644 --- a/seqan2.spec +++ b/seqan2.spec @@ -1,3 +1,5 @@ +%global __cmake_in_source_build 1 + # Tests need Python2 to be executed %global with_check 0 @@ -157,8 +159,33 @@ cp -p apps/rabema/COPYING apps/rabema/rabema-COPYING rm -rf util/py_lib/seqan/dox/tpl/lib/font-awesome/* %build +mkdir -p build/library && pushd build/library SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -%cmake -Wno-dev \ +%cmake \ + -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ + -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ + -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ + -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/%{name} \ + -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \ + -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \ + -DBUILD_SHARED_LIBS:BOOL=OFF \ + -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \ + -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \ + -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_LIBRARY \ + -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON \ + -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH=%{_libdir}/libz.so \ + -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH=%{_libdir}/libbz2.so \ + -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ + -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ + -DSPHINX_MAN_OUTPUT:BOOL=ON \ + -DSPHINX_TEXT_OUTPUT:BOOL=ON \ + -DYARA_LARGE_CONTIGS:BOOL=OFF ../.. +%make_build +popd + +mkdir -p build/Release && pushd build/Release +SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" +%cmake \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ @@ -176,11 +203,13 @@ SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -DYARA_LARGE_CONTIGS:BOOL=OFF \ -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ -DSPHINX_MAN_OUTPUT:BOOL=ON \ - -DSPHINX_TEXT_OUTPUT:BOOL=ON -%cmake_build + -DSPHINX_TEXT_OUTPUT:BOOL=ON ../.. +# Disable parallel Make jobs to prevent compiler errors +make -O -j1 %install -%cmake_install +%make_install -C build/library +%make_install -C build/Release # Unbundle font-awesome fonts %if 0%{?with_doc} From f7dd97f1161176357a0bf26694092cbea87838cf Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sun, 4 Feb 2024 17:41:15 +0100 Subject: [PATCH 6/6] Deprecated by seqan3 --- .gitignore | 2 - dead.package | 1 + seqan-disable_stripping.patch | 11 - seqan2-set_awk_installation.patch | 17 -- seqan2-set_config_filepath.patch | 24 -- seqan2.spec | 493 ------------------------------ sources | 1 - 7 files changed, 1 insertion(+), 548 deletions(-) delete mode 100644 .gitignore create mode 100644 dead.package delete mode 100644 seqan-disable_stripping.patch delete mode 100644 seqan2-set_awk_installation.patch delete mode 100644 seqan2-set_config_filepath.patch delete mode 100644 seqan2.spec delete mode 100644 sources diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 6d8e8ca..0000000 --- a/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -/seqan-8a875d71478a464de5ac3bcf2707f46819285a1f.zip -/seqan-seqan-v2.4.0.tar.gz diff --git a/dead.package b/dead.package new file mode 100644 index 0000000..05f1181 --- /dev/null +++ b/dead.package @@ -0,0 +1 @@ +Deprecated by seqan3 diff --git a/seqan-disable_stripping.patch b/seqan-disable_stripping.patch deleted file mode 100644 index 6b79443..0000000 --- a/seqan-disable_stripping.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- util/cmake/SeqAnBuildSystem.orig.cmake 2018-01-03 13:42:33.000000000 +0100 -+++ util/cmake/SeqAnBuildSystem.cmake 2018-01-06 17:12:26.494120190 +0100 -@@ -339,7 +339,7 @@ - (NOT SEQAN_BUILD_SYSTEM STREQUAL "DEVELOP") AND - (NOT APPLE) AND - (COMPILER_CLANG OR COMPILER_GCC)) -- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -s") -+ set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}") - endif () - - # search dependencies once, globally, if in DEVELOP diff --git a/seqan2-set_awk_installation.patch b/seqan2-set_awk_installation.patch deleted file mode 100644 index ef361d0..0000000 --- a/seqan2-set_awk_installation.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- apps/ngs_roi/CMakeLists.orig.txt 2018-01-03 13:42:33.000000000 +0100 -+++ apps/ngs_roi/CMakeLists.txt 2018-01-13 12:12:41.328240486 +0100 -@@ -86,9 +86,13 @@ - tool_shed/roi_sort.sh - # PDF plot script helper. - tool_shed/roi_plot_9.sh -+ DESTINATION ${CMAKE_INSTALL_BINDIR}) -+ -+# Install helper scripts into ${SHARE_INSTALL_PREFIX}/seqan2 directory. -+install (FILES # PDF plot script helper. - tool_shed/plot.awk - tool_shed/ps2pswLinks.gawk -- DESTINATION ${CMAKE_INSTALL_BINDIR}) -+ DESTINATION ${SHARE_INSTALL_PREFIX}/seqan2/pdf_plot_helper) - - # Install non-binary files for the package to "." for app builds and - # ${PREFIX}/share/doc/ngs_roi for SeqAn release builds. diff --git a/seqan2-set_config_filepath.patch b/seqan2-set_config_filepath.patch deleted file mode 100644 index 1a48e7d..0000000 --- a/seqan2-set_config_filepath.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- util/cmake/SeqAnBuildSystem.orig.cmake 2018-01-11 12:32:45.591134000 +0100 -+++ util/cmake/SeqAnBuildSystem.cmake 2018-01-11 12:51:55.193282581 +0100 -@@ -399,10 +399,10 @@ - # Install pkg-config file, except on Windows. - if (NOT CMAKE_SYSTEM_NAME MATCHES Windows) - configure_file("util/pkgconfig/seqan.pc.in" "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" @ONLY) -- install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/pkgconfig) -+ install(FILES "${CMAKE_BINARY_DIR}/util/pkgconfig/seqan-${SEQAN_VERSION_MAJOR}.pc" DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) - endif (NOT CMAKE_SYSTEM_NAME MATCHES Windows) - # Install FindSeqAn TODO(h-2) rename seqan-config.cmake to seqan-config${SEQAN_VERSION_MAJOR}.cmake after 2.x cycle -- install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/cmake/seqan/) -+ install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/util/cmake/seqan-config.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/seqan2/) - - # Install headers - file (GLOB HEADERS -@@ -473,7 +473,7 @@ - set (CMAKE_INSTALL_DOCDIR "${CMAKE_INSTALL_DATAROOTDIR}/doc" CACHE STRING "Documentation root (DATAROOTDIR/doc)" FORCE) - endif () - set (SEQAN_PREFIX_SHARE "${CMAKE_INSTALL_DATADIR}/${APP_NAME}") -- set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_DOCDIR}/${APP_NAME}") -+ set (SEQAN_PREFIX_SHARE_DOC "${CMAKE_INSTALL_PREFIX}/libexec/seqan2/examples/${APP_NAME}") - endif () - endmacro (seqan_setup_install_vars) - diff --git a/seqan2.spec b/seqan2.spec deleted file mode 100644 index 1c59c8a..0000000 --- a/seqan2.spec +++ /dev/null @@ -1,493 +0,0 @@ -%global __cmake_in_source_build 1 - -# Tests need Python2 to be executed -%global with_check 0 - -# Documentation needs Python2 to be built -%global with_doc 0 -Obsoletes: seqan2-doc < 0:2.4.0-8 - -Name: seqan2 -Summary: C++ library of efficient algorithms and data structures -Version: 2.4.0 -Release: 22%{?dist} -License: BSD-3-Clause -URL: https://www.seqan.de/ -Source0: https://github.com/seqan/seqan/archive/seqan-v%{version}.tar.gz#/seqan-seqan-v%{version}.tar.gz - -# Disable automatic stripping on no-DEVELOP seqan build systems -Patch0: seqan-disable_stripping.patch - -# Set paths of seqan-2.pc and seqan-config.cmake -Patch1: %{name}-set_config_filepath.patch - -# Set paths of plot.awk and ps2pswLinks.gawk files -Patch2: %{name}-set_awk_installation.patch - -# See https://fedoraproject.org/wiki/Changes/EncourageI686LeafRemoval -ExcludeArch: %{ix86} - -BuildRequires: make -BuildRequires: qt4-devel -BuildRequires: cmake, gcc-c++ -BuildRequires: llvm-devel -BuildRequires: bzip2-devel -BuildRequires: zlib-devel -BuildRequires: boost-devel -BuildRequires: libstdc++-static -BuildRequires: python3-devel - -## Test -%if 0%{?with_check} -BuildRequires: python3-nose -BuildRequires: python3-pytest -BuildRequires: python3-jinja2 -%endif - -## Bundled files exception https://fedorahosted.org/fpc/ticket/174 -Provides: bundled(gnulib) - -%description -SeqAn (version 2.x.x) 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. - -As such, it contains algorithms and data structures for - - * string representation and their manipluation, - * online and indexed string search, - * efficient I/O of bioinformatics file formats, - * sequence alignments, and - * many, many more. - - -%package apps -Summary: SeqAn (2.x.x) applications -## Seqan apps are licensed under BSD and GPLv3+ and LGPLv3+. -# BSD (3-clauses): alf, bs_tools, fiona, fx_tools, gustaf -# insegt, mason2, ngs_roi, param_chooser, rabema, razers3 -# sak, sam2matrix, samcat, searchjoin, seqcons2, yara -# ngs_roi, pair_align, ngs_roi. -# GPLv3+: rabema. -# LGPLv3+: dfi, insegt, micro_razers, pair_align -# param_chooser, razers, razers3, rep_sep, sak -# seqan_tcoffee, sgip, snp_store, splazers, stellar -# tree_recon. -# LGPLv3 gives you permission to relicense the code under GPLv3 -# BSD (3-clauses) is compatible with GPLv3 -# We can use a collective license: -License: GPL-3.0-or-later AND BSD-3-Clause AND LGPL-3.0-or-later -Requires: gawk%{?_isa} -Obsoletes: seqan <= 0:1.4.2 -Provides: seqan = 0:%{version}-%{release} - -%description apps -All SeqAn applications. - - -%package headers -Summary: SeqAn (2.x.x) headers only files - -# bzip2stream and zipstream libraries are distributed under zlib/libpng -# basic/boost*.h libraries are distributed under Boost -# bam_io/bam_index_bai.h is distributed under MIT -# Although Boost, zlib, MIT are GPL compatible, they're all tagged anyway -License: GPL-3.0-or-later AND BSD-3-Clause AND MIT AND LGPL-3.0-or-later AND Zlib AND BSL-1.0 - -Requires: bzip2-devel%{?_isa} -Requires: zlib-devel%{?_isa} -Provides: bundled(bzip2stream) -Provides: bundled(zipstream) - -%description headers -C headers files of SeqAn, including pkgconfig and CMake configuration files. - - -%package examples -Summary: SeqAn (2.x.x) examples -Requires: %{name}-apps%{?_isa} = %{version}-%{release} -%description examples -Testing files of SeqAn2's apps. - -%if 0%{?with_doc} -%package doc -Summary: SeqAn (2.x.x) documentation - -# 3L is licensed under MIT -# Less and bootstrap files is licensed under ASL 2.0 -# jquery-bbq are licensed under LGPLv3+ -License: LGPL-3.0-or-later AND MIT AND Apache-2.0 -BuildRequires: python3-sphinx -BuildRequires: python3-sphinx_rtd_theme -%if 0%{?fedora} > 38 -Requires: fontawesome4-fonts-web -%else -Requires: fontawesome-fonts-web -%endif -BuildArch: noarch - -# https://github.com/mateuszkocz/3l -Provides: bundled(3l) = 1.4.4 - -# http://lesscss.org/ -Provides: bundled(less) = 1.3.3 - -# http://twbs.github.com/bootstrap -Provides: bundled(bootstrap) = 3.0.0 - -Obsoletes: seqan-doc <= 0:1.4.2 -Provides: seqan-doc = 0:%{version}-%{release} -%description doc -Info files of SeqAn2's apps. -%endif - -%prep -%autosetup -p0 -n seqan-seqan-v%{version} - -## Remove spurious executable permissions -find . -perm /755 -type f \( -name "*.cpp" -o -name "*.h" \) -exec chmod -x {} ';' - -## Renamed each single license file -for appID in `ls apps/ | grep -v CMakeLists`; do - cp -p apps/$appID/LICENSE apps/$appID/$appID-LICENSE -done -cp -p apps/rabema/COPYING apps/rabema/rabema-COPYING - -# Unbundle font-awesome fonts -rm -rf util/py_lib/seqan/dox/tpl/lib/font-awesome/* - -%build -mkdir -p build/library && pushd build/library -SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -%cmake \ - -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ - -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ - -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ - -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/%{name} \ - -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \ - -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \ - -DBUILD_SHARED_LIBS:BOOL=OFF \ - -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES \ - -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \ - -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_LIBRARY \ - -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON \ - -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH=%{_libdir}/libz.so \ - -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH=%{_libdir}/libbz2.so \ - -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ - -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ - -DSPHINX_MAN_OUTPUT:BOOL=ON \ - -DSPHINX_TEXT_OUTPUT:BOOL=ON \ - -DYARA_LARGE_CONTIGS:BOOL=OFF ../.. -%make_build -popd - -mkdir -p build/Release && pushd build/Release -SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS" -%cmake \ - -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS -DNDEBUG" \ - -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ - -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/%{name} \ - -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/%{name} \ - -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 \ - -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_APPS \ - -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON \ - -DZLIB_INCLUDE_DIR:PATH=%{_includedir} -DZLIB_LIBRARY:FILEPATH=%{_libdir}/libz.so \ - -DBZIP2_INCLUDE_DIR:PATH=%{_includedir} -DBZIP2_LIBRARY:FILEPATH=%{_libdir}/libbz2.so \ - -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ - -DYARA_LARGE_CONTIGS:BOOL=OFF \ - -DSPHINX_EXECUTABLE:FILEPATH=%{_bindir}/sphinx-build \ - -DSPHINX_MAN_OUTPUT:BOOL=ON \ - -DSPHINX_TEXT_OUTPUT:BOOL=ON ../.. -# Disable parallel Make jobs to prevent compiler errors -make -O -j1 - -%install -%make_install -C build/library -%make_install -C build/Release - -# Unbundle font-awesome fonts -%if 0%{?with_doc} -ln -s %{_datadir}/font-awesome-web/scss %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/scss -ln -s %{_datadir}/font-awesome-web/css %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/css -ln -s %{_datadir}/fonts/fontawesome %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/fonts -ln -s %{_datadir}/font-awesome-web/less %{buildroot}%{_pkgdocdir}/html/lib/font-awesome/less -%endif - -## Fix executable permissions -chmod a+x %{buildroot}%{_bindir}/* - -# Set permissions and make symlinks of plot.awk and ps2pswLinks.gawk files -ln -s %{_datadir}/%{name}/pdf_plot_helper/plot.awk %{buildroot}%{_bindir}/plot.awk -ln -s %{_datadir}/%{name}/pdf_plot_helper/ps2pswLinks.gawk %{buildroot}%{_bindir}/ps2pswLinks.gawk - -## Remove unnecessary files -rm -rf %{buildroot}%{_libexecdir}/seqan2/examples/ngs_roi/R -rm -f %{buildroot}%{_datadir}/doc/seqan2/LICENSE -rm -f %{buildroot}%{_datadir}/doc/seqan2/CHANGELOG.rst -rm -f %{buildroot}%{_datadir}/doc/seqan2/README.rst - -%if 0%{?with_check} -%check -%ctest -- -E app_test_fiona -%endif - -%files apps -%license LICENSE -%license apps/*/*-LICENSE apps/rabema/rabema-COPYING -%doc README.rst CHANGELOG.rst -%{_bindir}/* -%{_mandir}/man1/* -%dir %{_datadir}/%{name} -%dir %{_datadir}/%{name}/pdf_plot_helper -%defattr(0444, root, root) -%{_datadir}/%{name}/pdf_plot_helper/plot.awk -%{_datadir}/%{name}/pdf_plot_helper/ps2pswLinks.gawk - -%files headers -%license include/seqan/LICENSE -%doc README.rst CHANGELOG.rst -%{_includedir}/%{name}/ -%{_libdir}/cmake/%{name}/ -%{_libdir}/pkgconfig/seqan-2.pc - -%files examples -%{_libexecdir}/%{name}/ -%exclude %{_libexecdir}/%{name}/examples/*/LICENSE - -%if 0%{?with_doc} -%files doc -%license LICENSE -%doc README.rst CHANGELOG.rst -%{_pkgdocdir}/ -%endif - -%changelog -* Mon Jan 29 2024 Jerry James - 2.4.0-22 -- Remove unused dependency on coin-or-lemon -- Convert License fields to SPDX -- Stop building for 32-bit x86 -- Depend on fontawesome4 for F39+, not fontawesome -- The headers subpackage needs bzip2-devel and zlib-devel -- Fix a few typos - -* Sat Jan 27 2024 Fedora Release Engineering - 2.4.0-21 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild - -* Sat Jul 22 2023 Fedora Release Engineering - 2.4.0-20 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild - -* Sat Jan 21 2023 Fedora Release Engineering - 2.4.0-19 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild - -* Sat Jul 23 2022 Fedora Release Engineering - 2.4.0-18 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild - -* Sun Jul 10 2022 Antonio Trande - 2.4.0-17 -- Drop Java dependency (rhbz#2104101) - -* Sat Feb 05 2022 Jiri Vanek - 2.4.0-16 -- Rebuilt for java-17-openjdk as system jdk - -* Sat Jan 22 2022 Fedora Release Engineering - 2.4.0-15 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild - -* Fri Jul 23 2021 Fedora Release Engineering - 2.4.0-14 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild - -* Tue Mar 30 2021 Jonathan Wakely - 2.4.0-13 -- Rebuilt for removed libstdc++ symbol (#1937698) - -* Wed Jan 27 2021 Fedora Release Engineering - 2.4.0-12 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild - -* Sat Aug 01 2020 Fedora Release Engineering - 2.4.0-11 -- Second attempt - Rebuilt for - https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Wed Jul 29 2020 Fedora Release Engineering - 2.4.0-10 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Thu Jan 30 2020 Fedora Release Engineering - 2.4.0-9 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild - -* Fri Nov 15 2019 Antonio Trande - 2.4.0-8 -- Switch to Python3 -- Disable documentation build -- Disable check - -* Sat Feb 02 2019 Fedora Release Engineering - 2.4.0-7 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild - -* Mon Oct 15 2018 Miro Hrončok - 2.4.0-6 -- Remove build dependency on python2-sphinxcontrib-bibtex - -* Sun Oct 07 2018 Antonio Trande - 2.4.0-5 -- Undefine ld_as_needed flag - -* Sat Jul 14 2018 Fedora Release Engineering - 2.4.0-4 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild - -* Wed Mar 07 2018 Adam Williamson - 2.4.0-3 -- Rebuild to fix GCC 8 mis-compilation - See https://da.gd/YJVwk ("GCC 8 ABI change on x86_64") - -* Fri Feb 09 2018 Fedora Release Engineering - 2.4.0-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild - -* Fri Feb 02 2018 Antonio Trande - 2.4.0-1 -- Update to version 2.4.0 - -* Wed Jan 17 2018 Antonio Trande - 2.4.0-0.4.20180103git8a875d -- Fix dependencies - -* Tue Jan 16 2018 Antonio Trande - 2.4.0-0.3.20180103git8a875d -- Split off applications in a single sub-package -- Devel rpm renamed seqan-headers - -* Sat Jan 13 2018 Antonio Trande - 2.4.0-0.2.20180103git8a875d -- plot.awk/ps2pswLinks.gawk installed in a private share datadir -- plot.awk/ps2pswLinks.gawk symliked in '_bindir' -- Renamed each single license file - -* Wed Jan 10 2018 Antonio Trande - 2.4.0-0.1.20180103git8a875d -- Pre-released as seqan-2.4.0 -- Add gcc-c++ BR -- Remove unnecessary R files -- Unbundle font-awesome -- Apps/libraries licensing commented - -* Mon Jan 08 2018 Antonio Trande - 2.3.2-3.20180103git8a875d -- Documentation still disabled - -* Wed Jan 03 2018 Antonio Trande - 2.3.2-2.20180103git8a875d -- Build devel commit #8a875d -- Add manually -DNDEBUG flag - -* Wed Sep 20 2017 Antonio Trande - 2.3.2-1 -- Update to 2.3.2 - -* 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 e5459d5..0000000 --- a/sources +++ /dev/null @@ -1 +0,0 @@ -SHA512 (seqan-seqan-v2.4.0.tar.gz) = f92cfc97304581920850c5d49fe4336f7c3855e99c3bcb035b6172fa7307e08e6f06fb06d1cd8f5b447c3220fc7f669684fbfe25641b43e9f6953999cf9ddd4b