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head/biology/htslib/files/patch-Makefile
| --- Makefile.orig 2016-04-22 08:45:12 UTC | --- Makefile.orig 2017-10-18 08:03:33 UTC | ||||
| +++ Makefile | +++ Makefile | ||||
| @@ -22,16 +22,7 @@ | @@ -22,41 +22,26 @@ | ||||
| # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER | # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER | ||||
| # DEALINGS IN THE SOFTWARE. | # DEALINGS IN THE SOFTWARE. | ||||
| -CC = gcc | -CC = gcc | ||||
| -AR = ar | -AR = ar | ||||
| -RANLIB = ranlib | -RANLIB = ranlib | ||||
| - | - | ||||
| -# Default libraries to link if configure is not used | |||||
| -htslib_default_libs = -lz -lm -lbz2 -llzma | |||||
| - | |||||
| -CPPFLAGS = | -CPPFLAGS = | ||||
| -# TODO: probably update cram code to make it compile cleanly with -Wc++-compat | -# TODO: probably update cram code to make it compile cleanly with -Wc++-compat | ||||
| -# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 | |||||
| -#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ | |||||
| -CFLAGS = -g -Wall -O2 | -CFLAGS = -g -Wall -O2 | ||||
| EXTRA_CFLAGS_PIC = -fpic | EXTRA_CFLAGS_PIC = -fpic | ||||
| -LDFLAGS = | -LDFLAGS = | ||||
| -LIBS = | -LIBS = $(htslib_default_libs) | ||||
| # For now these don't work too well as samtools also needs to know to | -prefix = /usr/local | ||||
| # add -lbz2 and -llzma if linking against the static libhts.a library. | +prefix = ${PREFIX} | ||||
| @@ -58,17 +49,11 @@ includedir = $(prefix)/include | exec_prefix = $(prefix) | ||||
| bindir = $(exec_prefix)/bin | |||||
| includedir = $(prefix)/include | |||||
| libdir = $(exec_prefix)/lib | libdir = $(exec_prefix)/lib | ||||
| libexecdir = $(exec_prefix)/libexec | libexecdir = $(exec_prefix)/libexec | ||||
| datarootdir = $(prefix)/share | datarootdir = $(prefix)/share | ||||
| -mandir = $(datarootdir)/man | -mandir = $(datarootdir)/man | ||||
| +mandir = $(prefix)/man | +mandir = $(prefix)/man | ||||
| man1dir = $(mandir)/man1 | man1dir = $(mandir)/man1 | ||||
| man5dir = $(mandir)/man5 | man5dir = $(mandir)/man5 | ||||
| pkgconfigdir= $(prefix)/libdata/pkgconfig | pkgconfigdir= $(prefix)/libdata/pkgconfig | ||||
| -MKDIR_P = mkdir -p | MKDIR_P = mkdir -p | ||||
| -INSTALL = install -p | -INSTALL = install -p | ||||
| -INSTALL_PROGRAM = $(INSTALL) | |||||
| -INSTALL_DATA = $(INSTALL) -m 644 | -INSTALL_DATA = $(INSTALL) -m 644 | ||||
| -INSTALL_DIR = $(MKDIR_P) -m 755 | -INSTALL_DIR = $(MKDIR_P) -m 755 | ||||
| - | -INSTALL_LIB = $(INSTALL_DATA) | ||||
| -INSTALL_MAN = $(INSTALL_DATA) | |||||
| -INSTALL_PROGRAM = $(INSTALL) | |||||
| +INSTALL_DATA = ${BSD_INSTALL_DATA} | |||||
| +INSTALL_DIR = $(MKDIR_P) | |||||
| +INSTALL_LIB = ${BSD_INSTALL_LIB} | |||||
| +INSTALL_MAN = ${BSD_INSTALL_MAN} | |||||
| +INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} | |||||
| # Set by config.mk if plugins are enabled | # Set by config.mk if plugins are enabled | ||||
| plugindir = | plugindir = | ||||
| @@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \ | |||||
| test/thrash_threads5 \ | |||||
| test/thrash_threads6 | |||||
| @@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \ | |||||
| test/test-vcf-api \ | |||||
| test/test-vcf-sweep | |||||
| -all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) | -all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) | ||||
| +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins | +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins | ||||
| HTSPREFIX = | HTSPREFIX = | ||||
| include htslib_vars.mk | include htslib_vars.mk | ||||
| @@ -360,7 +345,7 @@ installdirs: | |||||
| # and libhts.so.NN (used by client executables at runtime). | |||||
| install-so: libhts.so installdirs | |||||
| - $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) | |||||
| + $(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) | |||||
| ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so | |||||
| ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) | |||||