[gentoo-commits] proj/sci:master commit in: sci-biology/kat/files/
commit: 2ae549fb69309b8ab8537b3e9a8ea158d375cf1d
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon May 7 22:33:06 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon May 7 22:33:06 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2ae549fb
sci-biology/kat: removing patches for 2.4.1 version
Package-Manager: Portage-2.3.31, Repoman-2.3.9
.../kat/files/kat-2.4.1-make_no_pykat.patch| 15
.../kat/files/kat-2.4.1-no_static_build.patch | 43 --
2 files changed, 58 deletions(-)
diff --git a/sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch
b/sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch
deleted file mode 100644
index 7ba08010c..0
--- a/sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index 5f0f42e..4da6c05 100644
a/Makefile.am
-+++ b/Makefile.am
-@@ -21,10 +21,6 @@ dist_noinst_SCRIPTS = autogen.sh antigen.sh build_boost.sh
- # SRC DIRS
- make_dirs=deps/jellyfish-2.2.0 deps/seqan-library-2.0.0 lib src tests
-
--if MAKE_PYKAT
--make_dirs += scripts
--endif
--
- if MAKE_DOCS
- make_dirs += doc
- endif
diff --git a/sci-biology/kat/files/kat-2.4.1-no_static_build.patch
b/sci-biology/kat/files/kat-2.4.1-no_static_build.patch
deleted file mode 100644
index c8ac6c901..0
--- a/sci-biology/kat/files/kat-2.4.1-no_static_build.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/configure.ac b/configure.ac
-index b68c514..00c8a2e 100644
a/configure.ac
-+++ b/configure.ac
-@@ -159,11 +159,11 @@ if [[ "${make_pykat}" == "yes" ]]; then
- AM_CPPFLAGS="${ZLIB_CPPFLAGS} ${PYTHON_CPPFLAGS}"
- AM_LIBS="${PTHREAD_CFLAGS} ${ZLIB_LIB} ${RT_LIB} ${PYTHON_EXTRA_LIBS}
${PYTHON_LIBS}"
- #AM_LDFLAGS="${ZLIB_LDFLAGS} ${PYTHON_EXTRA_LDFLAGS} ${PYTHON_RPATH}
-static-libstdc++"
--AM_LDFLAGS="${ZLIB_LDFLAGS} -static-libstdc++ ${PYTHON_RPATH}"
-+AM_LDFLAGS="${ZLIB_LDFLAGS} ${PYTHON_RPATH}"
- else
- AM_CPPFLAGS="${ZLIB_CPPFLAGS}"
- AM_LIBS="${PTHREAD_CFLAGS} ${ZLIB_LIB} ${RT_LIB}"
--AM_LDFLAGS="${ZLIB_LDFLAGS} -static-libstdc++"
-+AM_LDFLAGS="${ZLIB_LDFLAGS}"
- fi
-
- AC_SUBST([AM_CPPFLAGS])
-diff --git a/deps/jellyfish-2.2.0/Makefile.am
b/deps/jellyfish-2.2.0/Makefile.am
-index 8f6fffd..d6e0a3d 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 = $(ZLIB_LDFLAGS) $(ZLIB_LIB) -lpthread -static-libstdc++ #
$(VALGRIND_LIBS)
-+AM_LDFLAGS = $(ZLIB_LDFLAGS) $(ZLIB_LIB) -lpthread # $(VALGRIND_LIBS)
- AM_CPPFLAGS = $(ZLIB_CPPFLAGS) -I$(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 a2ae071..71def5c 100644
a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -19,7 +19,6 @@ kat_CPPFLAGS = \
- @AM_CPPFLAGS@
-
- kat_LDFLAGS = \
-- -static \
- @AM_LDFLAGS@
-
- kat_LDADD = \
[gentoo-commits] proj/sci:master commit in: sci-biology/kat/files/, sci-biology/kat/
commit: f373141b6dd59db5eaf1bce4104e5ba6085958ac
Author: François Bissey gmail com>
AuthorDate: Mon Apr 23 08:51:16 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon May 7 21:44:57 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f373141b
sci-biology/kat: various fixes for issue #867
many thanks to @kiwifb and @maplesond for on fixing the package and ebuild
ax_check_zlib is in use. A hint for zlib location has to be provided
otherwise system zlib will be used on prefix.
make sure zlib is a dependency. develop branch has switched to proper
library detection.
fixing rpath. enabling python support (but broken right now).
make sure a suitable python3 is setup at configure time
bump to 2.4.2
fix typo in /DEPPEND/DEPEND/, cleanup comments
Closes: https://github.com/gentoo/sci/issues/867
Closes: https://github.com/gentoo/sci/pull/868
Package-Manager: Portage-2.3.31, Repoman-2.3.9
.../kat/files/kat-2.4.1-do-not-run-setup.py.patch | 30 --
.../kat/files/kat-2.4.1-ignore-bundled-deps.patch | 101 -
.../kat/files/kat-2.4.1-make_no_pykat.patch| 15 +++
.../kat/files/kat-2.4.1-no_static_build.patch | 43 +
.../kat/files/kat-2.4.2-ignore-bundled-deps.patch | 79
.../kat/files/kat-2.4.2-no_static_build.patch | 56
sci-biology/kat/kat-2.4.1.ebuild | 69 --
sci-biology/kat/kat-2.4.2.ebuild | 78
sci-biology/kat/kat-.ebuild| 60 +++-
sci-biology/kat/metadata.xml | 4 -
10 files changed, 307 insertions(+), 228 deletions(-)
diff --git a/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch
b/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch
deleted file mode 100644
index a00c971a6..0
--- a/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch
+++ /dev/null
@@ -1,30 +0,0 @@
scripts/Makefile.am.ori2018-04-22 16:02:12.829046527 +0200
-+++ scripts/Makefile.am2018-04-22 16:05:31.444532061 +0200
-@@ -1,27 +1,6 @@
- AUTOMAKE_OPTIONS = subdir-objects
-
-
--if MAKE_PYKAT_INSTALL
--
--install-exec-hook:
-- export PYTHONPATH=$(prefix)/lib/python$(PYTHON_VERSION)/site-packages
&& \
-- mkdir -p $(prefix)/lib/python$(PYTHON_VERSION)/site-packages/ && \
-- python3 setup.py install --prefix=$(prefix) --record install_files.txt
--
--uninstall-hook:
-- cat install_files.txt | xargs rm -rf
--
--else
--
--install-exec-hook:
-- mkdir -p $(prefix)/lib/python$(PYTHON_VERSION)/local/ && \
-- cp -r kat $(prefix)/lib/python$(PYTHON_VERSION)/local
--
--uninstall-hook:
-- rm -rf $(prefix)/lib/python$(PYTHON_VERSION)/local
--
--endif
--
- EXTRA_DIST = \
- kat/distanalysis.py \
- kat/plot/__init__.py \
diff --git a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
deleted file mode 100644
index 649f3ecd8..0
--- a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
+++ /dev/null
@@ -1,101 +0,0 @@
configure.ac.ori 2018-04-22 12:19:37.318794996 +0200
-+++ configure.ac 2018-04-22 12:20:43.310663598 +0200
-@@ -172,8 +172,8 @@
-
-
- AC_CONFIG_HEADERS([config.h])
--AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc
lib/Makefile src/Makefile tests/Makefile tests/compat.sh
deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py
scripts/Makefile])
--AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
-+AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc
lib/Makefile src/Makefile tests/Makefile tests/compat.sh
deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py
scripts/Makefile])
-+AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
- AC_OUTPUT
-
- pystr="detected ${PYTHON_VERSION}. Plotting and downstream analysis enabled."
lib/Makefile.am.ori2018-04-22 15:30:34.983653065 +0200
-+++ lib/Makefile.am2018-04-22 15:30:46.143961300 +0200
-@@ -7,8 +7,7 @@
-
- libkat_la_LDFLAGS = \
- -version-info 2:4:0 \
-- -L../deps/jellyfish-2.2.0 \
-- -L../deps/boost/build/lib
-+ -L../deps/jellyfish-2.2.0
-
- libkat_la_SOURCES = \
- src/matrix_metadata_extractor.cc \
-@@ -31,7 +30,6 @@
-
- libkat_la_CPPFLAGS = \
- -I$(top_srcdir)/deps/jellyfish-2.2.0/include \
-- -I$(top_srcdir)/deps/boost/build/include \
- -I$(top_srcdir)/lib/include \
- -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \
- @AM_CPPFLAGS@
src/Makefile.am.ori2018-04-22 15:30:46.203962959 +0200
-+++ src/Makefile.am2018-04-22 15:31:41.385487008 +0200
-@@ -14,7 +14,6 @@
- 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 \
-
[gentoo-commits] proj/sci:master commit in: sci-biology/kat/files/, sci-biology/kat/
commit: 8ee8fd95880516f79f8693c728d0ec218fa82277
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sun Apr 22 11:45:10 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 22 11:45:10 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8ee8fd95
sci-biology/kat: ignore site-wide boost-build/site-config.jam
Introduce - ebuild which zaps bundled stuff altogether and uses
system-wide boost and jellyfish2 files.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
.../kat/files/kat-2.4.1-ignore-bundled-deps.patch | 120
.../kat/files/kat-2.4.1-rename-jellyfish.patch | 159 +
sci-biology/kat/kat-2.4.1.ebuild | 7 +-
.../kat/{kat-.ebuild => kat-.ebuild} | 23 +--
sci-biology/kat/kat-.ebuild| 7 +-
5 files changed, 300 insertions(+), 16 deletions(-)
diff --git a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
new file mode 100644
index 0..d1816498e
--- /dev/null
+++ b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
@@ -0,0 +1,120 @@
+--- configure.ac.ori 2018-04-22 12:19:37.318794996 +0200
configure.ac 2018-04-22 12:20:43.310663598 +0200
+@@ -172,8 +172,8 @@
+
+
+ AC_CONFIG_HEADERS([config.h])
+-AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc
lib/Makefile src/Makefile tests/Makefile tests/compat.sh
deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py
scripts/Makefile])
+-AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
++AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc
lib/Makefile src/Makefile tests/Makefile tests/compat.sh scripts/setup.py
scripts/kat/__init__.py scripts/Makefile])
++AC_CONFIG_SUBDIRS([])
+ AC_OUTPUT
+
+ pystr="detected ${PYTHON_VERSION}. Plotting and downstream analysis enabled."
+--- Makefile.am.ori2018-04-22 12:23:58.756197763 +0200
Makefile.am2018-04-22 12:24:21.176832618 +0200
+@@ -19,7 +19,7 @@
+ dist_noinst_SCRIPTS = autogen.sh antigen.sh build_boost.sh
+
+ # SRC DIRS
+-make_dirs=deps/jellyfish-2.2.0 deps/seqan-library-2.0.0 lib src tests
++make_dirs=lib src tests
+
+ if MAKE_PYKAT
+ make_dirs += scripts
+--- tests/Makefile.am.ori 2018-04-22 12:31:02.738203085 +0200
tests/Makefile.am 2018-04-22 12:34:15.043648336 +0200
+@@ -29,8 +29,7 @@
+
+ AM_CPPFLAGS = \
+ -I$(top_srcdir)/lib/include \
+- -I$(top_srcdir)/deps/seqan-library-2.0.0/include \
+- -I$(top_srcdir)/deps/jellyfish-2.2.0/include \
++ -I$(top_srcdir)/usr/include/seqan-2.2 \
+ -I$(top_srcdir)/deps/boost/build/include \
+ -DDATADIR=\"$(srcdir)/data\" \
+ -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \
+@@ -60,7 +59,6 @@
+ -static \
+ -L. \
+ -L../lib \
+- -L../deps/jellyfish-2.2.0 \
+ -L../deps/boost/build/lib \
+ @AM_LDFLAGS@
+
+@@ -69,11 +67,11 @@
+ -lgtest \
+ -lkat \
+ -lkat_jellyfish \
+- ../deps/boost/build/lib/libboost_timer.a \
+-../deps/boost/build/lib/libboost_chrono.a \
+-../deps/boost/build/lib/libboost_filesystem.a \
+-../deps/boost/build/lib/libboost_program_options.a \
+-../deps/boost/build/lib/libboost_system.a \
++ -lboost_timer \
++ -lboost_chrono \
++ -lboost_filesystem \
++ -lboost_program_options \
++ -lboost_system \
+ @AM_LIBS@
+
+ include gtest.mk
+--- src/Makefile.am.ori2018-04-22 12:34:41.874408065 +0200
src/Makefile.am2018-04-22 12:36:33.567570728 +0200
+@@ -12,9 +12,7 @@
+ @AM_CXXFLAGS@
+
+ kat_CPPFLAGS = \
+- -I$(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/usr/include/seqan-2.2 \
+ -I$(top_srcdir)/lib/include \
+ -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \
+ @AM_CPPFLAGS@
+@@ -22,18 +20,16 @@
+ kat_LDFLAGS = \
+ -static \
+ -L../lib \
+- -L../deps/jellyfish-2.2.0 \
+- -L../deps/boost/build/lib \
+ @AM_LDFLAGS@
+
+ kat_LDADD = \
+ -lkat \
+ -lkat_jellyfish \
+- ../deps/boost/build/lib/libboost_timer.a \
+- ../deps/boost/build/lib/libboost_chrono.a \
+- ../deps/boost/build/lib/libboost_filesystem.a \
+- ../deps/boost/build/lib/libboost_program_options.a \
+- ../deps/boost/build/lib/libboost_system.a \
++ -lboost_timer \
++ -lboost_chrono \
++ -lboost_filesystem \
++ -lboost_program_options \
++ -lboost_system \
+ @AM_LIBS@
+
+ noinst_HEADERS = \
+--- lib/Makefile.am.ori2018-04-22 12:38:29.680858551 +0200
lib/Makefile.am2018-04-22 12:38:58.401671799 +0200
+@@ -6,9 +6,7 @@
+ lib_LTLIBRARIES = libkat.la
+
+ libkat_la_LDFLAGS = \
+- -version-info 2:4:0 \
+-
