* [gentoo-commits] gentoo-x86 commit in sci-biology/snpfile/files: snpfile-2.0.1-gentoo.diff
@ 2010-06-20 16:58 Kacper Kowalik (xarthisius)
0 siblings, 0 replies; 2+ messages in thread
From: Kacper Kowalik (xarthisius) @ 2010-06-20 16:58 UTC (permalink / raw
To: gentoo-commits
xarthisius 10/06/20 16:58:42
Added: snpfile-2.0.1-gentoo.diff
Log:
Fixing as-needed issues wrt bug 294971, provide shared libs. Thanks Diego for reporting.
(Portage version: 2.1.8.3/cvs/Linux x86_64)
Revision Changes Path
1.1 sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff?rev=1.1&content-type=text/plain
Index: snpfile-2.0.1-gentoo.diff
===================================================================
Fixing as-needed issues, provide shared libs
https://bugs.gentoo.org/show_bug.cgi?id=294971
--- Makefile.am
+++ Makefile.am
@@ -1,440 +1,91 @@
ACLOCAL_AMFLAGS = -I m4
-AM_CXXFLAGS =
-AM_CXXFLAGS += -Wall
-AM_CXXFLAGS += $(BOOST_CPPFLAGS)
+AM_CXXFLAGS = -Wall $(BOOST_CPPFLAGS)
-
-# for testing
-AM_CXXFLAGS += -g -O2 #-lefence
-
-# for profiling
-#CXXFLAGS += -O3 -g -pg
-#AM_CXXFLAGS += -O3 -g -pg
-
-# for production
-#CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG
-#AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG
-
-# for coverage testing
-#CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations
-#AM_CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations
-
-
-lib_LIBRARIES = libsnpfile.a
+lib_LTLIBRARIES = libsnpfile.la
noinst_PROGRAMS =
-TESTS =
-EXTRA_DIST =
-bin_PROGRAMS =
# conversion tools
-bin_PROGRAMS += text2snpfile
-bin_PROGRAMS += snpfile2text
-bin_PROGRAMS += snpfile2fastPHASE
-bin_PROGRAMS += fastPHASE2snpfile
-bin_PROGRAMS += snpfile2haploview
-bin_PROGRAMS += beagle_phase_snpfile
+bin_PROGRAMS = text2snpfile snpfile2text snpfile2fastPHASE fastPHASE2snpfile \
+ snpfile2haploview beagle_phase_snpfile
# data extraction tools
-bin_PROGRAMS += snpfile_genotype_count
-bin_PROGRAMS += snpfile_phenotypes
-bin_PROGRAMS += snpfile_markers
-
-bin_PROGRAMS += snpfile_metadata_info
-bin_PROGRAMS += snpfile_set_metadata
-bin_PROGRAMS += snpfile_get_metadata
+bin_PROGRAMS += snpfile_genotype_count snpfile_phenotypes snpfile_markers
+
+bin_PROGRAMS += snpfile_metadata_info snpfile_set_metadata snpfile_get_metadata
# other tools
noinst_PROGRAMS += snpfile_split_on_column
# tests
-noinst_PROGRAMS += matrix_test
-TESTS += matrix_test
-noinst_PROGRAMS += file_test
-TESTS += file_test
-noinst_PROGRAMS += file_matrix_test
-TESTS += file_matrix_test
-noinst_PROGRAMS += readonly_matrix_test
-TESTS += readonly_matrix_test
-noinst_PROGRAMS += archives_test
-TESTS += archives_test
-noinst_PROGRAMS += metadata_access_test
-TESTS += metadata_access_test
-noinst_PROGRAMS += metadata_types_test
-TESTS += metadata_types_test
-noinst_PROGRAMS += iterators_test
-TESTS += iterators_test
-noinst_PROGRAMS += tabulate_test
-TESTS += tabulate_test
-noinst_PROGRAMS += metadata_filtering_test
-TESTS += metadata_filtering_test
+TESTS = matrix_test file_test file_matrix_test readonly_matrix_test archives_test \
+ metadata_access_test metadata_types_test iterators_test tabulate_test metadata_filtering_test
+
+noinst_PROGRAMS += $(TESTS)
#Utils for testing across different machines
-noinst_PROGRAMS += make_test_snpfile
-noinst_PROGRAMS += test_test_snpfile
+noinst_PROGRAMS += make_test_snpfile test_test_snpfile
# other experiments...
-noinst_PROGRAMS += row_metadata_experiment
-noinst_PROGRAMS += metadata_cache_prototype
-noinst_PROGRAMS += matrix_benchmark
-noinst_PROGRAMS += matrix_benchmark_write
-noinst_PROGRAMS += matrix_benchmark_read
-
-
-
-matrix_test_LDADD =
-matrix_test_LDADD += $(BOOST_SIGNALS_LIB)
-matrix_test_SOURCES =
-matrix_test_SOURCES += test_util.hh test_util.cc
-matrix_test_SOURCES += matrix.hh matrix.cc
-matrix_test_SOURCES += array_matrix.hh array_matrix.cc
-matrix_test_SOURCES += file_matrix.hh file_matrix.cc
-matrix_test_SOURCES += input_archive.hh
-matrix_test_SOURCES += output_archive.hh
-matrix_test_SOURCES += metadata.hh metadata.cc
-matrix_test_SOURCES += snpfile.hh snpfile.cc
-matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
-matrix_test_SOURCES += matrix_test.cc
-
-
-file_test_LDADD =
-file_test_LDADD += $(BOOST_SIGNALS_LIB)
-file_test_SOURCES =
-file_test_SOURCES += test_util.hh test_util.cc
-file_test_SOURCES += metadata.hh metadata.cc
-file_test_SOURCES += snpfile.hh snpfile.cc
-file_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
-file_test_SOURCES += file_test.cc
-file_test_SOURCES += metadata_access.hh
-file_test_SOURCES += input_archive.hh
-file_test_SOURCES += output_archive.hh
-
-file_matrix_test_LDADD =
-file_matrix_test_LDADD += $(BOOST_SIGNALS_LIB)
-file_matrix_test_SOURCES =
-file_matrix_test_SOURCES += test_util.hh test_util.cc
-file_matrix_test_SOURCES += file_matrix.hh file_matrix.cc
-file_matrix_test_SOURCES += matrix.hh matrix.cc
-file_matrix_test_SOURCES += input_archive.hh
-file_matrix_test_SOURCES += output_archive.hh
-file_matrix_test_SOURCES += metadata.hh metadata.cc
-file_matrix_test_SOURCES += snpfile.hh snpfile.cc
-file_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
-file_matrix_test_SOURCES += file_matrix_test.cc
-
-
-readonly_matrix_test_LDADD =
-readonly_matrix_test_LDADD += $(BOOST_SIGNALS_LIB)
-readonly_matrix_test_SOURCES =
-readonly_matrix_test_SOURCES += test_util.hh test_util.cc
-readonly_matrix_test_SOURCES += array_matrix.hh array_matrix.cc
-readonly_matrix_test_SOURCES += file_matrix.hh file_matrix.cc
-readonly_matrix_test_SOURCES += matrix.hh matrix.cc
-readonly_matrix_test_SOURCES += input_archive.hh
-readonly_matrix_test_SOURCES += output_archive.hh
-readonly_matrix_test_SOURCES += metadata.hh metadata.cc
-readonly_matrix_test_SOURCES += snpfile.hh snpfile.cc
-readonly_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
-readonly_matrix_test_SOURCES += readonly_matrix_test.cc
-
-
-archives_test_SOURCES =
-archives_test_SOURCES += input_archive.hh
-archives_test_SOURCES += output_archive.hh
-archives_test_SOURCES += archives_test.cc
-
-
-metadata_access_test_LDADD =
-metadata_access_test_LDADD += $(BOOST_SIGNALS_LIB)
-metadata_access_test_SOURCES =
-metadata_access_test_SOURCES += test_util.hh test_util.cc
-metadata_access_test_SOURCES += metadata.hh metadata.cc
-metadata_access_test_SOURCES += snpfile.hh snpfile.cc
-metadata_access_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
-metadata_access_test_SOURCES += input_archive.hh
-metadata_access_test_SOURCES += output_archive.hh
-metadata_access_test_SOURCES += serialization_trait.hh
-metadata_access_test_SOURCES += metadata_access_test.cc
-
-
-metadata_types_test_LDADD =
-metadata_types_test_LDADD += $(BOOST_SIGNALS_LIB)
-metadata_types_test_SOURCES =
-metadata_types_test_SOURCES += test_util.hh test_util.cc
-metadata_types_test_SOURCES += metadata.hh metadata.cc
-metadata_types_test_SOURCES += snpfile.hh snpfile.cc
-metadata_types_test_SOURCES += byte_order_handler.hh byte_order_handler.cc
-metadata_types_test_SOURCES += input_archive.hh
-metadata_types_test_SOURCES += output_archive.hh
-metadata_types_test_SOURCES += serialization_trait.hh
-metadata_types_test_SOURCES += metadata_types_test.cc
-
-
-iterators_test_SOURCES =
-iterators_test_SOURCES += iterators.hh
-iterators_test_SOURCES += array_matrix.hh array_matrix.cc
-iterators_test_SOURCES += matrix.hh matrix.cc
-iterators_test_SOURCES += iterators_test.cc
-
-
-tabulate_test_SOURCES =
-tabulate_test_SOURCES += tabulate.hh
-tabulate_test_SOURCES += array_matrix.hh array_matrix.cc
-tabulate_test_SOURCES += matrix.hh matrix.cc
-tabulate_test_SOURCES += tabulate_test.cc
-
-
-metadata_filtering_test_SOURCES =
-metadata_filtering_test_SOURCES += matrix.hh matrix.cc
-metadata_filtering_test_SOURCES += array_matrix.hh array_matrix.cc
-metadata_filtering_test_SOURCES += metadata_filtering.hh
-metadata_filtering_test_SOURCES += metadata_filtering_test.cc
-
-
-make_test_snpfile_LDADD =
-make_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB)
-make_test_snpfile_SOURCES =
-make_test_snpfile_SOURCES += metadata.hh metadata.cc
-make_test_snpfile_SOURCES += snpfile.hh snpfile.cc
-make_test_snpfile_SOURCES += matrix.hh matrix.cc
-make_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc
-make_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc
-make_test_snpfile_SOURCES += input_archive.hh
-make_test_snpfile_SOURCES += output_archive.hh
-make_test_snpfile_SOURCES += make_test_snpfile.cc
-
-
-test_test_snpfile_LDADD =
-test_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB)
-test_test_snpfile_SOURCES =
-test_test_snpfile_SOURCES += metadata.hh metadata.cc
-test_test_snpfile_SOURCES += snpfile.hh snpfile.cc
-test_test_snpfile_SOURCES += matrix.hh matrix.cc
-test_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc
-test_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc
-test_test_snpfile_SOURCES += input_archive.hh
-test_test_snpfile_SOURCES += output_archive.hh
-test_test_snpfile_SOURCES += test_test_snpfile.cc
-
-
-row_metadata_experiment_LDADD =
-row_metadata_experiment_LDADD += $(BOOST_SIGNALS_LIB)
-row_metadata_experiment_SOURCES =
-row_metadata_experiment_SOURCES += matrix.hh matrix.cc
-row_metadata_experiment_SOURCES += array_matrix.hh array_matrix.cc
-row_metadata_experiment_SOURCES += file_matrix.hh file_matrix.cc
-row_metadata_experiment_SOURCES += input_archive.hh
-row_metadata_experiment_SOURCES += output_archive.hh
-row_metadata_experiment_SOURCES += metadata.hh metadata.cc
-row_metadata_experiment_SOURCES += snpfile.hh snpfile.cc
-row_metadata_experiment_SOURCES += byte_order_handler.hh byte_order_handler.cc
-row_metadata_experiment_SOURCES += test_util.hh test_util.cc
-row_metadata_experiment_SOURCES += row_metadata_experiment.cc
-
-
-metadata_cache_prototype_SOURCES =
-metadata_cache_prototype_SOURCES += metadata_cache_prototype.cc
-metadata_cache_prototype_LDFLAGS =
-metadata_cache_prototype_LDFLAGS += -L.
-metadata_cache_prototype_LDADD =
-metadata_cache_prototype_LDADD += $(BOOST_SIGNALS_LIB)
-metadata_cache_prototype_LDADD += -lsnpfile
-
-
-matrix_benchmark_LDADD =
-matrix_benchmark_LDADD += $(BOOST_SIGNALS_LIB)
-matrix_benchmark_SOURCES =
-matrix_benchmark_SOURCES += test_util.hh test_util.cc
-matrix_benchmark_SOURCES += file_matrix.hh file_matrix.cc
-matrix_benchmark_SOURCES += array_matrix.hh array_matrix.cc
-matrix_benchmark_SOURCES += matrix.hh matrix.cc
-matrix_benchmark_SOURCES += input_archive.hh
-matrix_benchmark_SOURCES += output_archive.hh
-matrix_benchmark_SOURCES += metadata.hh metadata.cc
-matrix_benchmark_SOURCES += snpfile.hh snpfile.cc
-matrix_benchmark_SOURCES += byte_order_handler.hh byte_order_handler.cc
-matrix_benchmark_SOURCES += timing.hh timing.cc
-matrix_benchmark_SOURCES += matrix_benchmark.cc
-
-
-matrix_benchmark_write_LDADD =
-matrix_benchmark_write_LDADD += $(BOOST_SIGNALS_LIB)
-matrix_benchmark_write_SOURCES =
-matrix_benchmark_write_SOURCES += file_matrix.hh file_matrix.cc
-matrix_benchmark_write_SOURCES += matrix.hh matrix.cc
-matrix_benchmark_write_SOURCES += input_archive.hh
-matrix_benchmark_write_SOURCES += output_archive.hh
-matrix_benchmark_write_SOURCES += metadata.hh metadata.cc
-matrix_benchmark_write_SOURCES += snpfile.hh snpfile.cc
-matrix_benchmark_write_SOURCES += byte_order_handler.hh byte_order_handler.cc
-matrix_benchmark_write_SOURCES += timing.hh timing.cc
-matrix_benchmark_write_SOURCES += matrix_benchmark_write.cc
-
-
-matrix_benchmark_read_LDADD =
-matrix_benchmark_read_LDADD += $(BOOST_SIGNALS_LIB)
-matrix_benchmark_read_SOURCES =
-matrix_benchmark_read_SOURCES += file_matrix.hh file_matrix.cc
-matrix_benchmark_read_SOURCES += matrix.hh matrix.cc
-matrix_benchmark_read_SOURCES += input_archive.hh
-matrix_benchmark_read_SOURCES += output_archive.hh
-matrix_benchmark_read_SOURCES += metadata.hh metadata.cc
-matrix_benchmark_read_SOURCES += snpfile.hh snpfile.cc
-matrix_benchmark_read_SOURCES += byte_order_handler.hh byte_order_handler.cc
-matrix_benchmark_read_SOURCES += timing.hh timing.cc
-matrix_benchmark_read_SOURCES += matrix_benchmark_read.cc
+noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \
+ matrix_benchmark_write matrix_benchmark_read
+
+LDADD = $(top_builddir)/libsnpfile.la
+
+matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc
+
+file_test_SOURCES = test_util.hh test_util.cc file_test.cc metadata_access.hh input_archive.hh \
+ output_archive.hh
+
+file_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
+ file_matrix_test.cc
+
+readonly_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
+ readonly_matrix_test.cc
+archives_test_SOURCES = input_archive.hh output_archive.hh archives_test.cc
+
+metadata_access_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
+ serialization_trait.hh metadata_access_test.cc
+
+metadata_types_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \
+ serialization_trait.hh metadata_types_test.cc
+
+iterators_test_SOURCES = iterators.hh iterators_test.cc
+
+tabulate_test_SOURCES = tabulate.hh tabulate_test.cc
+
+metadata_filtering_test_SOURCES = metadata_filtering.hh metadata_filtering_test.cc
+
+make_test_snpfile_SOURCES = input_archive.hh output_archive.hh make_test_snpfile.cc
+
+test_test_snpfile_SOURCES = input_archive.hh output_archive.hh test_test_snpfile.cc
+
+row_metadata_experiment_SOURCES = input_archive.hh output_archive.hh test_util.hh test_util.cc \
+ row_metadata_experiment.cc
+
+matrix_benchmark_SOURCES = test_util.hh test_util.cc input_archive.hh \
+ output_archive.hh timing.hh timing.cc matrix_benchmark.cc
+
+matrix_benchmark_write_SOURCES = input_archive.hh output_archive.hh \
+ timing.hh timing.cc matrix_benchmark_write.cc
+
+matrix_benchmark_read_SOURCES = input_archive.hh output_archive.hh \
+ timing.hh timing.cc matrix_benchmark_read.cc
+
+snpfile_genotype_count_SOURCES = genotype_count.cc
snpfileincludedir = $(includedir)/snpfile
-snpfileinclude_HEADERS =
-snpfileinclude_HEADERS += common.hh
-snpfileinclude_HEADERS += matrix.hh
-snpfileinclude_HEADERS += file_matrix.hh
-snpfileinclude_HEADERS += array_matrix.hh
-snpfileinclude_HEADERS += byte_order_handler.hh
-snpfileinclude_HEADERS += metadata.hh
-snpfileinclude_HEADERS += metadata_access.hh
-snpfileinclude_HEADERS += archive_common.hh
-snpfileinclude_HEADERS += archives.hh
-snpfileinclude_HEADERS += input_archive.hh
-snpfileinclude_HEADERS += output_archive.hh
-snpfileinclude_HEADERS += snpfile.hh
-snpfileinclude_HEADERS += serialization_trait.hh
-snpfileinclude_HEADERS += type_trait.hh
-snpfileinclude_HEADERS += iterators.hh
-snpfileinclude_HEADERS += tabulate.hh
-
-libsnpfile_a_SOURCES =
-libsnpfile_a_SOURCES += common.hh
-libsnpfile_a_SOURCES += matrix.hh matrix.cc
-libsnpfile_a_SOURCES += file_matrix.hh file_matrix.cc
-libsnpfile_a_SOURCES += array_matrix.cc array_matrix.hh
-libsnpfile_a_SOURCES += byte_order_handler.cc byte_order_handler.hh
-libsnpfile_a_SOURCES += metadata.hh metadata.cc metadata_access.hh
-libsnpfile_a_SOURCES += archive_common.hh
-libsnpfile_a_SOURCES += archives.hh
-libsnpfile_a_SOURCES += input_archive.hh
-libsnpfile_a_SOURCES += output_archive.hh
-libsnpfile_a_SOURCES += snpfile.hh snpfile.cc
-libsnpfile_a_SOURCES += serialization_trait.hh
-libsnpfile_a_SOURCES += type_trait.hh
-
-text2snpfile_SOURCES =
-text2snpfile_SOURCES += text2snpfile.cc
-text2snpfile_LDFLAGS =
-text2snpfile_LDFLAGS += -L.
-text2snpfile_LDADD =
-text2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-text2snpfile_LDADD += $(BOOST_SIGNALS_LIB)
-text2snpfile_LDADD += -lsnpfile
-
-snpfile2text_SOURCES =
-snpfile2text_SOURCES += snpfile2text.cc
-snpfile2text_LDFLAGS =
-snpfile2text_LDFLAGS += -L.
-snpfile2text_LDADD =
-snpfile2text_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-snpfile2text_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile2text_LDADD += -lsnpfile
-
-
-snpfile2fastPHASE_SOURCES =
-snpfile2fastPHASE_SOURCES += snpfile2fastPHASE.cc
-snpfile2fastPHASE_LDFLAGS =
-snpfile2fastPHASE_LDFLAGS += -L.
-snpfile2fastPHASE_LDADD =
-snpfile2fastPHASE_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-snpfile2fastPHASE_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile2fastPHASE_LDADD += -lsnpfile
-
-fastPHASE2snpfile_SOURCES =
-fastPHASE2snpfile_SOURCES += fastPHASE2snpfile.cc
-fastPHASE2snpfile_LDFLAGS =
-fastPHASE2snpfile_LDFLAGS += -L.
-fastPHASE2snpfile_LDADD =
-fastPHASE2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-fastPHASE2snpfile_LDADD += $(BOOST_SIGNALS_LIB)
-fastPHASE2snpfile_LDADD += -lsnpfile
-
-
-snpfile2haploview_SOURCES =
-snpfile2haploview_SOURCES += snpfile2haploview.cc
-snpfile2haploview_LDFLAGS =
-snpfile2haploview_LDFLAGS += -L.
-snpfile2haploview_LDADD =
-snpfile2haploview_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-snpfile2haploview_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile2haploview_LDADD += -lsnpfile
-
-
-beagle_phase_snpfile_SOURCES =
-beagle_phase_snpfile_SOURCES += beagle_phase_snpfile.cc
-beagle_phase_snpfile_LDFLAGS =
-beagle_phase_snpfile_LDFLAGS += -L.
-beagle_phase_snpfile_LDADD =
-beagle_phase_snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-beagle_phase_snpfile_LDADD += $(BOOST_SIGNALS_LIB)
-beagle_phase_snpfile_LDADD += -lsnpfile
-
-snpfile_genotype_count_SOURCES =
-snpfile_genotype_count_SOURCES += genotype_count.cc
-snpfile_genotype_count_LDFLAGS =
-snpfile_genotype_count_LDFLAGS += -L.
-snpfile_genotype_count_LDADD =
-snpfile_genotype_count_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-snpfile_genotype_count_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile_genotype_count_LDADD += -lsnpfile
-
-snpfile_phenotypes_SOURCES =
-snpfile_phenotypes_SOURCES += snpfile_phenotypes.cc
-snpfile_phenotypes_LDFLAGS =
-snpfile_phenotypes_LDFLAGS += -L.
-snpfile_phenotypes_LDADD =
-snpfile_phenotypes_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-snpfile_phenotypes_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile_phenotypes_LDADD += -lsnpfile
-
-snpfile_markers_SOURCES =
-snpfile_markers_SOURCES += snpfile_markers.cc
-snpfile_markers_LDFLAGS =
-snpfile_markers_LDFLAGS += -L.
-snpfile_markers_LDADD =
-snpfile_markers_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-snpfile_markers_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile_markers_LDADD += -lsnpfile
-
-snpfile_metadata_info_SOURCES =
-snpfile_metadata_info_SOURCES += snpfile_metadata_info.cc
-snpfile_metadata_info_LDFLAGS =
-snpfile_metadata_info_LDFLAGS += -L.
-snpfile_metadata_info_LDADD =
-snpfile_metadata_info_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile_metadata_info_LDADD += -lsnpfile
-
-snpfile_set_metadata_SOURCES =
-snpfile_set_metadata_SOURCES += snpfile_set_metadata.cc
-snpfile_set_metadata_LDFLAGS =
-snpfile_set_metadata_LDFLAGS += -L.
-snpfile_set_metadata_LDADD =
-snpfile_set_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-snpfile_set_metadata_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile_set_metadata_LDADD += -lsnpfile
-
-snpfile_get_metadata_SOURCES =
-snpfile_get_metadata_SOURCES += snpfile_get_metadata.cc
-snpfile_get_metadata_LDFLAGS =
-snpfile_get_metadata_LDFLAGS += -L.
-snpfile_get_metadata_LDADD =
-snpfile_get_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-snpfile_get_metadata_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile_get_metadata_LDADD += -lsnpfile
-
-snpfile_split_on_column_SOURCES =
-snpfile_split_on_column_SOURCES += snpfile_split_on_column.cc
-snpfile_split_on_column_LDFLAGS =
-snpfile_split_on_column_LDFLAGS += -L.
-snpfile_split_on_column_LDADD =
-snpfile_split_on_column_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
-snpfile_split_on_column_LDADD += $(BOOST_SIGNALS_LIB)
-snpfile_split_on_column_LDADD += -lsnpfile
+snpfileinclude_HEADERS = common.hh matrix.hh file_matrix.hh array_matrix.hh \
+ byte_order_handler.hh metadata.hh metadata_access.hh archive_common.hh \
+ archives.hh input_archive.hh output_archive.hh snpfile.hh serialization_trait.hh \
+ type_trait.hh iterators.hh tabulate.hh
+
+libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix.cc \
+ array_matrix.cc array_matrix.hh byte_order_handler.cc byte_order_handler.hh \
+ metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \
+ input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \
+ type_trait.hh
+libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB)
+
--- configure.in
+++ configure.in
@@ -1,10 +1,11 @@
AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk)
AM_INIT_AUTOMAKE
+AC_CONFIG_MACRO_DIR([m4])
AM_CONFIG_HEADER(config.hh)
+LT_INIT
AC_PROG_CXX
AC_PROG_INSTALL
-AC_PROG_RANLIB
if test "x$prefix" != xNONE; then
thePREFIX=$prefix
^ permalink raw reply [flat|nested] 2+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/snpfile/files: snpfile-2.0.1-gentoo.diff
@ 2010-10-02 7:52 Kacper Kowalik (xarthisius)
0 siblings, 0 replies; 2+ messages in thread
From: Kacper Kowalik (xarthisius) @ 2010-10-02 7:52 UTC (permalink / raw
To: gentoo-commits
xarthisius 10/10/02 07:52:04
Modified: snpfile-2.0.1-gentoo.diff
Log:
Fix patch to compile with make-3.82 wrt bug 336542. Thanks to Diego for the report.
(Portage version: 2.1.9/cvs/Linux x86_64)
Revision Changes Path
1.2 sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff?r1=1.1&r2=1.2
Index: snpfile-2.0.1-gentoo.diff
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- snpfile-2.0.1-gentoo.diff 20 Jun 2010 16:58:41 -0000 1.1
+++ snpfile-2.0.1-gentoo.diff 2 Oct 2010 07:52:04 -0000 1.2
@@ -4,14 +4,15 @@
--- Makefile.am
+++ Makefile.am
-@@ -1,440 +1,91 @@
+@@ -1,440 +1,92 @@
ACLOCAL_AMFLAGS = -I m4
-AM_CXXFLAGS =
-AM_CXXFLAGS += -Wall
-AM_CXXFLAGS += $(BOOST_CPPFLAGS)
+AM_CXXFLAGS = -Wall $(BOOST_CPPFLAGS)
-
++SUFFIXES = .cc
+
-
-# for testing
-AM_CXXFLAGS += -g -O2 #-lefence
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2010-10-02 7:52 [gentoo-commits] gentoo-x86 commit in sci-biology/snpfile/files: snpfile-2.0.1-gentoo.diff Kacper Kowalik (xarthisius)
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