diff options
Diffstat (limited to 'sci-biology/kat/files')
| -rw-r--r-- | sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch | 79 | ||||
| -rw-r--r-- | sci-biology/kat/files/kat-2.4.2-no_static_build.patch | 56 |
2 files changed, 0 insertions, 135 deletions
diff --git a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch b/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch deleted file mode 100644 index 46d343294..000000000 --- a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch +++ /dev/null @@ -1,79 +0,0 @@ -diff --git a/lib/Makefile.am b/lib/Makefile.am -index ac23917..0ca4be9 100644 ---- a/lib/Makefile.am -+++ b/lib/Makefile.am -@@ -6,7 +6,6 @@ pkgconfig_DATA = kat.pc - lib_LTLIBRARIES = libkat.la - - libkat_la_LDFLAGS = \ -- -L$(top_builddir)/deps/boost/build/lib/ \ - -version-info 2:4:2 - - LIBS = \ -@@ -41,7 +40,6 @@ library_include_HEADERS = $(KI)/distance_metrics.hpp \ - - libkat_la_CPPFLAGS = \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -I$(top_srcdir)/lib/include \ - -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ - @AM_CPPFLAGS@ -diff --git a/src/Makefile.am b/src/Makefile.am -index 1cdf7e0..dfa878b 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -14,7 +14,6 @@ kat_CXXFLAGS = \ - kat_CPPFLAGS = \ - -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -I$(top_srcdir)/lib/include \ - -DKAT_SCRIPTS='"$(datarootdir)/scripts"' \ - -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ -@@ -25,13 +24,13 @@ kat_LDFLAGS = \ - @AM_LDFLAGS@ - - kat_LDADD = \ -- $(top_builddir)/deps/boost/build/lib/libboost_timer.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_chrono.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_filesystem.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_program_options.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_system.a \ -- $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ - $(top_builddir)/lib/libkat.la \ -+ $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ -+ -lboost_timer \ -+ -lboost_chrono \ -+ -lboost_filesystem \ -+ -lboost_program_options \ -+ -lboost_system \ - @AM_LIBS@ - - noinst_HEADERS = \ -diff --git a/tests/Makefile.am b/tests/Makefile.am -index eee4e8b..dec2a5f 100644 ---- a/tests/Makefile.am -+++ b/tests/Makefile.am -@@ -31,7 +31,6 @@ AM_CPPFLAGS = \ - -I$(top_srcdir)/lib/include \ - -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -DDATADIR=\"$(srcdir)/data\" \ - -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ - @AM_CPPFLAGS@ -@@ -58,13 +57,11 @@ check_unit_tests_SOURCES = \ - - check_unit_tests_LDFLAGS = \ - -static \ -- -L$(top_builddir)/deps/boost/build/lib \ -- -Wl,-rpath $(top_builddir)/deps/boost/build/lib \ - @AM_LDFLAGS@ - - check_unit_tests_LDADD = \ - libgtest.la \ -- $(top_builddir)/lib/libkat.la \ -+ $(top_builddir)/lib/libkat.la \ - -lboost_timer \ - -lboost_chrono \ - -lboost_filesystem \ diff --git a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch b/sci-biology/kat/files/kat-2.4.2-no_static_build.patch deleted file mode 100644 index 48ad6d562..000000000 --- a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch +++ /dev/null @@ -1,56 +0,0 @@ -diff --git a/configure.ac b/configure.ac -index 9acc141..24a4b14 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -178,8 +178,6 @@ define([PC_FILE], lib/kat-2.2.pc) - - AM_CXXFLAGS="-g -O2 -std=c++11" - AC_SUBST([AM_CXXFLAGS]) --AM_LDFLAGS="-static-libstdc++" --AC_SUBST([AM_LDFLAGS]) - - if [[ "${make_pykat}" == "yes" ]]; then - AM_CPPFLAGS="${PYTHON_CPPFLAGS}" -diff --git a/deps/jellyfish-2.2.0/Makefile.am b/deps/jellyfish-2.2.0/Makefile.am -index 83192d9..e3b1694 100644 ---- a/deps/jellyfish-2.2.0/Makefile.am -+++ b/deps/jellyfish-2.2.0/Makefile.am -@@ -7,7 +7,7 @@ man1_MANS = doc/kat_jellyfish.man - pkgconfigdir = $(libdir)/pkgconfig - pkgconfig_DATA = kat_jellyfish.pc - --AM_LDFLAGS = -lz -lpthread -static-libstdc++ # $(VALGRIND_LIBS) -+AM_LDFLAGS = -lz -lpthread # $(VALGRIND_LIBS) - AM_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/include # $(VALGRIND_CFLAGS) - AM_CXXFLAGS = $(ALL_CXXFLAGS) -Wall -Wnon-virtual-dtor -Wno-deprecated-declarations - -diff --git a/src/Makefile.am b/src/Makefile.am -index 2d5cd72..cb5cb0e 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -18,10 +18,6 @@ kat_CPPFLAGS = \ - -DKAT_SCRIPTS='"$(datadir)/scripts"' \ - @AM_CPPFLAGS@ - --kat_LDFLAGS = \ -- -static \ -- @AM_LDFLAGS@ -- - kat_LDADD = \ - $(top_builddir)/lib/libkat.la \ - $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ -diff --git a/tests/Makefile.am b/tests/Makefile.am -index d96363a..90e4f61 100644 ---- a/tests/Makefile.am -+++ b/tests/Makefile.am -@@ -54,10 +54,6 @@ check_unit_tests_SOURCES = \ - check_compcounters.cc \ - check_main.cc - --check_unit_tests_LDFLAGS = \ -- -static \ -- @AM_LDFLAGS@ -- - check_unit_tests_LDADD = \ - libgtest.la \ - $(top_builddir)/lib/libkat.la \ |