From a3a06298d3135241b35587728d8005c784f03a9b Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 9 Feb 2018 16:30:52 +0000 Subject: [PATCH 01/31] - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 9459656..287b9b8 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 33%{?dist} +Release: 34%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -151,6 +151,9 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags} %{_includedir}/seqan/ %changelog +* 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 From 366cdb35610be090b9164c63d3b5cd68d8a972a7 Mon Sep 17 00:00:00 2001 From: sagitter Date: Thu, 22 Feb 2018 21:52:38 +0100 Subject: [PATCH 02/31] Add gcc-c++ BR --- seqan.spec | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/seqan.spec b/seqan.spec index 287b9b8..fb0e274 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 34%{?dist} +Release: 35%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -14,6 +14,7 @@ Patch0: %{name}-docpath.patch 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 @@ -25,9 +26,9 @@ BuildRequires: libstdc++-static BuildRequires: java-1.8.0-openjdk-devel ## Test BuildRequires: python2-devel -BuildRequires: python-nose -BuildRequires: pytest -BuildRequires: python-jinja2 +BuildRequires: python2-nose +BuildRequires: python2-pytest +BuildRequires: python2-jinja2 Requires: gawk @@ -151,6 +152,9 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags} %{_includedir}/seqan/ %changelog +* 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 From f3ba892cee391fc13ed0377b3674fc98a19317e3 Mon Sep 17 00:00:00 2001 From: Adam Williamson Date: Wed, 7 Mar 2018 20:17:15 -0800 Subject: [PATCH 03/31] Rebuild to fix GCC 8 mis-compilation See https://da.gd/YJVwk ("GCC 8 ABI change on x86_64") --- seqan.spec | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index fb0e274..95e8dbb 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 35%{?dist} +Release: 36%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -152,6 +152,10 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags} %{_includedir}/seqan/ %changelog +* 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 From 0a836463e3e75c0f249860117eb98e22c5fabc03 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 14 Jul 2018 05:58:39 +0000 Subject: [PATCH 04/31] - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 95e8dbb..a0fa6fb 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 36%{?dist} +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 @@ -152,6 +152,9 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags} %{_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") From 744f80a84c45e65d95ba981c143f778703d7cc09 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 2 Feb 2019 15:12:11 +0000 Subject: [PATCH 05/31] - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index a0fa6fb..564cf4d 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 37%{?dist} +Release: 38%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -152,6 +152,9 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags} %{_includedir}/seqan/ %changelog +* Sat Feb 02 2019 Fedora Release Engineering - 1.4.2-38 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild + * Sat Jul 14 2018 Fedora Release Engineering - 1.4.2-37 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild From dc6362e432b38b95c6a13623ba06469de06ae412 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 26 Jul 2019 23:05:11 +0000 Subject: [PATCH 06/31] - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 564cf4d..9cd43d5 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 38%{?dist} +Release: 39%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -152,6 +152,9 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags} %{_includedir}/seqan/ %changelog +* Fri Jul 26 2019 Fedora Release Engineering - 1.4.2-39 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild + * Sat Feb 02 2019 Fedora Release Engineering - 1.4.2-38 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild From 57d2fcb85c43e7ba59ad58012a9b0ebaea5fd749 Mon Sep 17 00:00:00 2001 From: sagitter Date: Fri, 2 Aug 2019 13:55:55 +0200 Subject: [PATCH 07/31] Switch to Python3 --- seqan.spec | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/seqan.spec b/seqan.spec index 9cd43d5..9dec37c 100644 --- a/seqan.spec +++ b/seqan.spec @@ -16,7 +16,7 @@ Patch2: %{name}-exclude_bstools_test.patch BuildRequires: gcc, gcc-c++ BuildRequires: qt4-devel >= 4.7 -BuildRequires: cmake >= 2.8 +BuildRequires: cmake BuildRequires: llvm-devel BuildRequires: bzip2-devel BuildRequires: zlib-devel @@ -25,10 +25,11 @@ 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 +BuildRequires: python3-devel +BuildRequires: python3-sphinx +BuildRequires: python3-nose +BuildRequires: python3-pytest +BuildRequires: python3-jinja2 Requires: gawk @@ -64,9 +65,8 @@ Info files of SeqAn's apps. %endif ## Remove spurious executable permissions -for i in `find . -perm /111 -type f \( -name "*.h" -o -name "*.cpp" \)`; do -chmod a-x $i -done +find . -type f -name "*.h" -exec chmod 0644 '{}' \; +find . -type f -name "*.cpp" -exec chmod 0644 '{}' \; ## Renamed each single license file cp -p extras/apps/rep_sep/LICENSE LGPLv3+.txt @@ -80,7 +80,7 @@ cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README mkdir -p build/Release && pushd build/Release ##This error comes out on >=F22 ##cc1plus: out of memory -%ifarch %{arm} || ( 0%{?fedora} >= 22 ) +%ifarch %{arm} SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g') SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC -Wl,-z,now" %else @@ -101,7 +101,7 @@ cmake \ -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} \ + -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE ../.. ##Compiler fails with parallel make @@ -124,9 +124,7 @@ rm -f seqandoc/*.txt 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 +find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %check pushd build/Release @@ -152,8 +150,9 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags} %{_includedir}/seqan/ %changelog -* Fri Jul 26 2019 Fedora Release Engineering - 1.4.2-39 +* Fri Aug 02 2019 Fedora Release Engineering - 1.4.2-39 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild +- Switch to python3 * Sat Feb 02 2019 Fedora Release Engineering - 1.4.2-38 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild From 74f946018d6c5d8e7dc92652789e2f31f9f9a779 Mon Sep 17 00:00:00 2001 From: sagitter Date: Fri, 2 Aug 2019 14:40:44 +0200 Subject: [PATCH 08/31] Return to Python2 --- seqan.spec | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/seqan.spec b/seqan.spec index 9dec37c..6dfae9c 100644 --- a/seqan.spec +++ b/seqan.spec @@ -25,11 +25,11 @@ BuildRequires: coin-or-lemon-devel BuildRequires: libstdc++-static BuildRequires: java-1.8.0-openjdk-devel ## Test -BuildRequires: python3-devel -BuildRequires: python3-sphinx -BuildRequires: python3-nose -BuildRequires: python3-pytest -BuildRequires: python3-jinja2 +BuildRequires: python2-devel +BuildRequires: python2-sphinx +BuildRequires: python2-nose +BuildRequires: python2-pytest +BuildRequires: python2-jinja2 Requires: gawk @@ -152,7 +152,6 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags} %changelog * Fri Aug 02 2019 Fedora Release Engineering - 1.4.2-39 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild -- Switch to python3 * Sat Feb 02 2019 Fedora Release Engineering - 1.4.2-38 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild From 6408a8bd8c9a36f3c122f3a65df410cc8a59b789 Mon Sep 17 00:00:00 2001 From: sagitter Date: Fri, 2 Aug 2019 15:35:07 +0200 Subject: [PATCH 09/31] Do not perform the tests (need Python2 tools) --- seqan.spec | 33 ++++----------------------------- 1 file changed, 4 insertions(+), 29 deletions(-) diff --git a/seqan.spec b/seqan.spec index 6dfae9c..81f89e6 100644 --- a/seqan.spec +++ b/seqan.spec @@ -24,12 +24,6 @@ BuildRequires: boost-devel BuildRequires: coin-or-lemon-devel BuildRequires: libstdc++-static BuildRequires: java-1.8.0-openjdk-devel -## Test -BuildRequires: python2-devel -BuildRequires: python2-sphinx -BuildRequires: python2-nose -BuildRequires: python2-pytest -BuildRequires: python2-jinja2 Requires: gawk @@ -78,18 +72,7 @@ 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} -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" \ +%cmake \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \ -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \ @@ -105,10 +88,10 @@ cmake \ -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE ../.. ##Compiler fails with parallel make -make all +make -j1 all %install -%make_install -C build/Release INSTALL="install -p" +%make_install -C build/Release ## Put header files in ad-hoc include directory mkdir -p %{buildroot}%{_includedir}/seqan @@ -126,15 +109,6 @@ mv %{buildroot}%{_bindir}/join %{buildroot}%{_bindir}/searchjoin ## Fix executable permissions find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; -%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 @@ -152,6 +126,7 @@ ctest --force-new-ctest-process -VV %{?_smp_mflags} %changelog * Fri Aug 02 2019 Fedora Release Engineering - 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 - 1.4.2-38 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild From 43ffa4bcc943e9c4b47c2269fbc664832b1304c3 Mon Sep 17 00:00:00 2001 From: sagitter Date: Fri, 2 Aug 2019 15:36:18 +0200 Subject: [PATCH 10/31] Add python3-devel --- seqan.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/seqan.spec b/seqan.spec index 81f89e6..d5fff2b 100644 --- a/seqan.spec +++ b/seqan.spec @@ -24,6 +24,7 @@ BuildRequires: boost-devel BuildRequires: coin-or-lemon-devel BuildRequires: libstdc++-static BuildRequires: java-1.8.0-openjdk-devel +BuildRequires: python3-devel Requires: gawk From 4c052176d855800a0d38e5d57155b66dfefb6587 Mon Sep 17 00:00:00 2001 From: sagitter Date: Fri, 2 Aug 2019 18:09:00 +0200 Subject: [PATCH 11/31] Downgrade opt level on ARM --- seqan.spec | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index d5fff2b..0a170ca 100644 --- a/seqan.spec +++ b/seqan.spec @@ -73,7 +73,17 @@ cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README %build mkdir -p build/Release && pushd build/Release -%cmake \ +# cc1plus: out of memory on ARM +%ifarch %{arm} +SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g') +SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC" +%else +SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS -fPIC" +%endif +export CXXFLAGS="$SEQAN_OPT_FLAGS" +export LDFLAGS="$RPM_LD_FLAGS -fPIC" +cmake \ + -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS" \ -DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \ -DSYSCONF_INSTALL_DIR:PATH=%{_sysconfdir} \ -DSHARE_INSTALL_PREFIX:PATH=%{_datadir} \ From 75e0ff72fc1c0736c72f0b31ab22220b2c46034d Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 30 Jan 2020 23:14:18 +0000 Subject: [PATCH 12/31] - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 0a170ca..1df7094 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 39%{?dist} +Release: 40%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -135,6 +135,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Thu Jan 30 2020 Fedora Release Engineering - 1.4.2-40 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild + * Fri Aug 02 2019 Fedora Release Engineering - 1.4.2-39 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild - Do not perform the tests (need Python2 tools) From a0903efdd39deae6bf83f6cde34d5fe8431599f6 Mon Sep 17 00:00:00 2001 From: sagitter Date: Fri, 7 Feb 2020 12:34:57 +0100 Subject: [PATCH 13/31] Linker flag to liblemon --- seqan.spec | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/seqan.spec b/seqan.spec index 1df7094..cae9dc6 100644 --- a/seqan.spec +++ b/seqan.spec @@ -75,12 +75,12 @@ cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README mkdir -p build/Release && pushd build/Release # cc1plus: out of memory on ARM %ifarch %{arm} -SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g') +SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g' -e 's/-Werror=format-security//g') SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC" %else SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS -fPIC" %endif -export CXXFLAGS="$SEQAN_OPT_FLAGS" +export CXXFLAGS="$SEQAN_OPT_FLAGS -lemon" export LDFLAGS="$RPM_LD_FLAGS -fPIC" cmake \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS" \ @@ -98,7 +98,7 @@ cmake \ -DBoost_INCLUDE_DIR:PATH=%{_includedir} -DPYTHON_EXECUTABLE:FILEPATH=%{__python3} \ -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE ../.. -##Compiler fails with parallel make +## Compiler fails with parallel make make -j1 all %install @@ -135,8 +135,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog -* Thu Jan 30 2020 Fedora Release Engineering - 1.4.2-40 +* Fri Feb 07 2020 Antonio Trande - 1.4.2-40 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild +- Linker flag to liblemon * Fri Aug 02 2019 Fedora Release Engineering - 1.4.2-39 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild From 92a366477ae9fca0f4b753b224e4d1e50fb42028 Mon Sep 17 00:00:00 2001 From: sagitter Date: Fri, 7 Feb 2020 12:59:39 +0100 Subject: [PATCH 14/31] Remove -Wp,-D_FORTIFY_SOURCE=2 at opt-level 0 on ARM --- seqan.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index cae9dc6..23087c8 100644 --- a/seqan.spec +++ b/seqan.spec @@ -75,7 +75,7 @@ cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README mkdir -p build/Release && pushd build/Release # cc1plus: out of memory on ARM %ifarch %{arm} -SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g' -e 's/-Werror=format-security//g') +SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g' -e 's/-Wp,-D_FORTIFY_SOURCE=2//g') SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC" %else SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS -fPIC" From 254345d94971864654c64851267c4dd5b89570b3 Mon Sep 17 00:00:00 2001 From: sagitter Date: Wed, 24 Jun 2020 21:38:54 +0200 Subject: [PATCH 15/31] BuildRequires python3-setuptools explicitly --- seqan.spec | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 23087c8..8e3d3d9 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 40%{?dist} +Release: 41%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -25,6 +25,7 @@ BuildRequires: coin-or-lemon-devel BuildRequires: libstdc++-static BuildRequires: java-1.8.0-openjdk-devel BuildRequires: python3-devel +BuildRequires: python3-setuptools Requires: gawk @@ -135,6 +136,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Wed Jun 24 2020 Antonio Trande - 1.4.2-41 +- BuildRequires python3-setuptools + * Fri Feb 07 2020 Antonio Trande - 1.4.2-40 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild - Linker flag to liblemon From 9e59bafb9e2c55ca520a04be48ae4ce59cf2e5be Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 29 Jul 2020 10:32:57 +0000 Subject: [PATCH 16/31] - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 8e3d3d9..0d5e6c1 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 41%{?dist} +Release: 42%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -136,6 +136,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Wed Jul 29 2020 Fedora Release Engineering - 1.4.2-42 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + * Wed Jun 24 2020 Antonio Trande - 1.4.2-41 - BuildRequires python3-setuptools From 24b38ccbe2d5a38dc5500efa37061e692f1b981f Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 1 Aug 2020 09:01:32 +0000 Subject: [PATCH 17/31] - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 0d5e6c1..388e0f9 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,7 +1,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 42%{?dist} +Release: 43%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -136,6 +136,10 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Sat Aug 01 2020 Fedora Release Engineering - 1.4.2-43 +- Second attempt - Rebuilt for + https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + * Wed Jul 29 2020 Fedora Release Engineering - 1.4.2-42 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild From 7acd252c03d36bc6ccc7e63b84068e67eabd707d Mon Sep 17 00:00:00 2001 From: sagitter Date: Tue, 4 Aug 2020 22:15:30 +0200 Subject: [PATCH 18/31] Disable LTO flags --- seqan.spec | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/seqan.spec b/seqan.spec index 388e0f9..7bc9c5d 100644 --- a/seqan.spec +++ b/seqan.spec @@ -1,3 +1,7 @@ +# LTO flags prevent the linker's work +# /usr/bin/ld: error: lto-wrapper failed +%define _lto_cflags %{nil} + Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 From c644aa09a737b72ec5b7036360253b171ff75403 Mon Sep 17 00:00:00 2001 From: Jeff Law Date: Wed, 19 Aug 2020 12:43:41 -0600 Subject: [PATCH 19/31] Force C++14 as this code is not C++17 ready --- seqan.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/seqan.spec b/seqan.spec index 7bc9c5d..1f9426a 100644 --- a/seqan.spec +++ b/seqan.spec @@ -5,7 +5,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 43%{?dist} +Release: 44%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -85,7 +85,7 @@ SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC" %else SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS -fPIC" %endif -export CXXFLAGS="$SEQAN_OPT_FLAGS -lemon" +export CXXFLAGS="-std=c++14 $SEQAN_OPT_FLAGS -lemon" export LDFLAGS="$RPM_LD_FLAGS -fPIC" cmake \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="$SEQAN_OPT_FLAGS" \ @@ -140,6 +140,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Wed Aug 19 2020 Jeff Law - 1.4.2-44 +- Force C++14 as this code is not C++17 ready + * Sat Aug 01 2020 Fedora Release Engineering - 1.4.2-43 - Second attempt - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild From 451e4919a27e7033af46fdf5fc6b0d535ebde051 Mon Sep 17 00:00:00 2001 From: Tom Stellard Date: Fri, 8 Jan 2021 21:22:39 +0000 Subject: [PATCH 20/31] Add BuildRequires: make https://fedoraproject.org/wiki/Changes/Remove_make_from_BuildRoot --- seqan.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/seqan.spec b/seqan.spec index 1f9426a..cef428c 100644 --- a/seqan.spec +++ b/seqan.spec @@ -18,6 +18,7 @@ Patch0: %{name}-docpath.patch Patch1: %{name}-exclude_splazers_fiona_tests.patch Patch2: %{name}-exclude_bstools_test.patch +BuildRequires: make BuildRequires: gcc, gcc-c++ BuildRequires: qt4-devel >= 4.7 BuildRequires: cmake From 77eeefcf50cafc2b14a00cf86f2731acdbd63209 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 27 Jan 2021 20:13:08 +0000 Subject: [PATCH 21/31] - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index cef428c..ada9941 100644 --- a/seqan.spec +++ b/seqan.spec @@ -5,7 +5,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 44%{?dist} +Release: 45%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -141,6 +141,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Wed Jan 27 2021 Fedora Release Engineering - 1.4.2-45 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild + * Wed Aug 19 2020 Jeff Law - 1.4.2-44 - Force C++14 as this code is not C++17 ready From ac1dc05037de7fdd8993845fddd3193138ba537a Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 23 Jul 2021 17:22:23 +0000 Subject: [PATCH 22/31] - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index ada9941..8162679 100644 --- a/seqan.spec +++ b/seqan.spec @@ -5,7 +5,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 45%{?dist} +Release: 46%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -141,6 +141,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Fri Jul 23 2021 Fedora Release Engineering - 1.4.2-46 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + * Wed Jan 27 2021 Fedora Release Engineering - 1.4.2-45 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild From fa1b07eeb4ffcdcc8d05529887b47c12f5fcc8bf Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 22 Jan 2022 00:41:16 +0000 Subject: [PATCH 23/31] - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 8162679..2fb1c95 100644 --- a/seqan.spec +++ b/seqan.spec @@ -5,7 +5,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 46%{?dist} +Release: 47%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -141,6 +141,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Sat Jan 22 2022 Fedora Release Engineering - 1.4.2-47 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild + * Fri Jul 23 2021 Fedora Release Engineering - 1.4.2-46 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild From eedf7fdee151ae242681d161aa8c9a6ac1a3c980 Mon Sep 17 00:00:00 2001 From: Jiri Date: Sun, 6 Feb 2022 00:10:06 +0100 Subject: [PATCH 24/31] Rebuilt for java-17-openjdk as system jdk https://fedoraproject.org/wiki/Changes/Java17 --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 2fb1c95..c5970b5 100644 --- a/seqan.spec +++ b/seqan.spec @@ -5,7 +5,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 47%{?dist} +Release: 48%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -141,6 +141,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Sat Feb 05 2022 Jiri Vanek - 1.4.2-48 +- Rebuilt for java-17-openjdk as system jdk + * Sat Jan 22 2022 Fedora Release Engineering - 1.4.2-47 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild From 3d055faa62db6e66dc8966067624cda06e71e3d1 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Tue, 5 Jul 2022 17:52:43 +0200 Subject: [PATCH 25/31] Drop JDK in i686 builds --- seqan.spec | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index c5970b5..2064705 100644 --- a/seqan.spec +++ b/seqan.spec @@ -5,7 +5,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 48%{?dist} +Release: 49%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -28,7 +28,9 @@ BuildRequires: zlib-devel BuildRequires: boost-devel BuildRequires: coin-or-lemon-devel BuildRequires: libstdc++-static +%ifarch %{java_arches} BuildRequires: java-1.8.0-openjdk-devel +%endif BuildRequires: python3-devel BuildRequires: python3-setuptools @@ -141,6 +143,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Tue Jul 05 2022 Antonio Trande - 1.4.2-49 +- Drop JDK in i686 builds + * Sat Feb 05 2022 Jiri Vanek - 1.4.2-48 - Rebuilt for java-17-openjdk as system jdk From 5b16374bf2caf053a6a23493d70c10f089a82bab Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 23 Jul 2022 08:22:53 +0000 Subject: [PATCH 26/31] Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 2064705..4a67e59 100644 --- a/seqan.spec +++ b/seqan.spec @@ -5,7 +5,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 49%{?dist} +Release: 50%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -143,6 +143,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Sat Jul 23 2022 Fedora Release Engineering - 1.4.2-50 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild + * Tue Jul 05 2022 Antonio Trande - 1.4.2-49 - Drop JDK in i686 builds From 87daad9e2d92becb67535153ad478a21080b00c0 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Tue, 17 Jan 2023 18:07:42 +0100 Subject: [PATCH 27/31] Use _fortify_level (rhbz#2161371) --- seqan.spec | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/seqan.spec b/seqan.spec index 4a67e59..be53a86 100644 --- a/seqan.spec +++ b/seqan.spec @@ -2,10 +2,13 @@ # /usr/bin/ld: error: lto-wrapper failed %define _lto_cflags %{nil} +# %%_fortify_level +%undefine _fortify_level + Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 50%{?dist} +Release: 51%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -83,7 +86,7 @@ cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README mkdir -p build/Release && pushd build/Release # cc1plus: out of memory on ARM %ifarch %{arm} -SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g' -e 's/-Wp,-D_FORTIFY_SOURCE=2//g') +SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g') SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC" %else SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS -fPIC" @@ -143,6 +146,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Tue Jan 17 2023 Antonio Trande - 1.4.2-51 +- Use _fortify_level (rhbz#2161371) + * Sat Jul 23 2022 Fedora Release Engineering - 1.4.2-50 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild From 76ccc8ff92d9632b769650f5e3332fab985d56e1 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Fri, 20 Jan 2023 22:50:35 +0100 Subject: [PATCH 28/31] Reduce optimization level in i686 --- seqan.spec | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/seqan.spec b/seqan.spec index be53a86..fe22883 100644 --- a/seqan.spec +++ b/seqan.spec @@ -85,7 +85,7 @@ cp -p extras/apps/seqan_flexbar/INFO extras/apps/seqan_flexbar/README %build mkdir -p build/Release && pushd build/Release # cc1plus: out of memory on ARM -%ifarch %{arm} +%ifarch %{arm} %{ix86} SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g') SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC" %else @@ -146,8 +146,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog -* Tue Jan 17 2023 Antonio Trande - 1.4.2-51 +* Fri Jan 20 2023 Antonio Trande - 1.4.2-51 - Use _fortify_level (rhbz#2161371) +- Reduce optimization level in i686 * Sat Jul 23 2022 Fedora Release Engineering - 1.4.2-50 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild From ecbfe544f54de968546dd7975fe2ab9294748fbe Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 22 Jul 2023 01:25:22 +0000 Subject: [PATCH 29/31] Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index fe22883..346490e 100644 --- a/seqan.spec +++ b/seqan.spec @@ -8,7 +8,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 51%{?dist} +Release: 52%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -146,6 +146,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Sat Jul 22 2023 Fedora Release Engineering - 1.4.2-52 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild + * Fri Jan 20 2023 Antonio Trande - 1.4.2-51 - Use _fortify_level (rhbz#2161371) - Reduce optimization level in i686 From af4d1c77cf015c6cac3b24636ba03a37411f0fc5 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 27 Jan 2024 02:35:21 +0000 Subject: [PATCH 30/31] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild --- seqan.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/seqan.spec b/seqan.spec index 346490e..6b424c0 100644 --- a/seqan.spec +++ b/seqan.spec @@ -8,7 +8,7 @@ Name: seqan Summary: Open source C++ library of efficient algorithms and data structures Version: 1.4.2 -Release: 52%{?dist} +Release: 53%{?dist} License: BSD and GPLv3+ and LGPLv3+ URL: http://www.seqan.de/ Source0: http://packages.seqan.de/seqan-src/seqan-src-%{version}.tar.gz @@ -146,6 +146,9 @@ find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; %{_includedir}/seqan/ %changelog +* Sat Jan 27 2024 Fedora Release Engineering - 1.4.2-53 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + * Sat Jul 22 2023 Fedora Release Engineering - 1.4.2-52 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild From 1ab3726d611d7b83172aec60889c50a2c6908d71 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sun, 4 Feb 2024 12:57:29 +0100 Subject: [PATCH 31/31] No longer needed in Fedora; deprecated by seqan3 --- .gitignore | 4 - dead.package | 1 + seqan-docpath.patch | 11 - seqan-exclude_bstools_test.patch | 23 -- seqan-exclude_splazers_fiona_tests.patch | 23 -- seqan.spec | 332 ----------------------- sources | 1 - 7 files changed, 1 insertion(+), 394 deletions(-) delete mode 100644 .gitignore create mode 100644 dead.package delete mode 100644 seqan-docpath.patch delete mode 100644 seqan-exclude_bstools_test.patch delete mode 100644 seqan-exclude_splazers_fiona_tests.patch delete mode 100644 seqan.spec delete mode 100644 sources 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 6b424c0..0000000 --- a/seqan.spec +++ /dev/null @@ -1,332 +0,0 @@ -# LTO flags prevent the linker's work -# /usr/bin/ld: error: lto-wrapper failed -%define _lto_cflags %{nil} - -# %%_fortify_level -%undefine _fortify_level - -Name: seqan -Summary: Open source C++ library of efficient algorithms and data structures -Version: 1.4.2 -Release: 53%{?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: make -BuildRequires: gcc, gcc-c++ -BuildRequires: qt4-devel >= 4.7 -BuildRequires: cmake -BuildRequires: llvm-devel -BuildRequires: bzip2-devel -BuildRequires: zlib-devel -BuildRequires: boost-devel -BuildRequires: coin-or-lemon-devel -BuildRequires: libstdc++-static -%ifarch %{java_arches} -BuildRequires: java-1.8.0-openjdk-devel -%endif -BuildRequires: python3-devel -BuildRequires: python3-setuptools - -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 -find . -type f -name "*.h" -exec chmod 0644 '{}' \; -find . -type f -name "*.cpp" -exec chmod 0644 '{}' \; - -## 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 -# cc1plus: out of memory on ARM -%ifarch %{arm} %{ix86} -SEQAN_OPT_FLAGS=$(echo "$RPM_OPT_FLAGS" | sed -e 's/-O2/-O0/g') -SEQAN_OPT_FLAGS="$SEQAN_OPT_FLAGS -fPIC" -%else -SEQAN_OPT_FLAGS="$RPM_OPT_FLAGS -fPIC" -%endif -export CXXFLAGS="-std=c++14 $SEQAN_OPT_FLAGS -lemon" -export LDFLAGS="$RPM_LD_FLAGS -fPIC" -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=%{__python3} \ - -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE ../.. - -## Compiler fails with parallel make -make -j1 all - -%install -%make_install -C build/Release - -## 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 -find %{buildroot}%{_bindir} -type f -name "*.h" -exec chmod 0755 '{}' \; - -%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 Jan 27 2024 Fedora Release Engineering - 1.4.2-53 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild - -* Sat Jul 22 2023 Fedora Release Engineering - 1.4.2-52 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild - -* Fri Jan 20 2023 Antonio Trande - 1.4.2-51 -- Use _fortify_level (rhbz#2161371) -- Reduce optimization level in i686 - -* Sat Jul 23 2022 Fedora Release Engineering - 1.4.2-50 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild - -* Tue Jul 05 2022 Antonio Trande - 1.4.2-49 -- Drop JDK in i686 builds - -* Sat Feb 05 2022 Jiri Vanek - 1.4.2-48 -- Rebuilt for java-17-openjdk as system jdk - -* Sat Jan 22 2022 Fedora Release Engineering - 1.4.2-47 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild - -* Fri Jul 23 2021 Fedora Release Engineering - 1.4.2-46 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild - -* Wed Jan 27 2021 Fedora Release Engineering - 1.4.2-45 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild - -* Wed Aug 19 2020 Jeff Law - 1.4.2-44 -- Force C++14 as this code is not C++17 ready - -* Sat Aug 01 2020 Fedora Release Engineering - 1.4.2-43 -- Second attempt - Rebuilt for - https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Wed Jul 29 2020 Fedora Release Engineering - 1.4.2-42 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Wed Jun 24 2020 Antonio Trande - 1.4.2-41 -- BuildRequires python3-setuptools - -* Fri Feb 07 2020 Antonio Trande - 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 - 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 - 1.4.2-38 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild - -* 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