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biology/htslib/files/patch-Makefile
--- Makefile.orig 2015-12-15 16:34:33 UTC | --- Makefile.orig 2016-04-22 08:45:12 UTC | ||||
+++ Makefile | +++ Makefile | ||||
@@ -22,16 +22,7 @@ | @@ -22,16 +22,7 @@ | ||||
# 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 | ||||
- | - | ||||
-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 | ||||
-CFLAGS = -g -Wall -O2 | -CFLAGS = -g -Wall -O2 | ||||
EXTRA_CFLAGS_PIC = -fpic | EXTRA_CFLAGS_PIC = -fpic | ||||
-LDFLAGS = | -LDFLAGS = | ||||
-LIBS = | -LIBS = | ||||
# For now these don't work too well as samtools also needs to know to | # For now these don't work too well as samtools also needs to know to | ||||
# add -lbz2 and -llzma if linking against the static libhts.a library. | # add -lbz2 and -llzma if linking against the static libhts.a library. | ||||
@@ -58,16 +49,10 @@ includedir = $(prefix)/include | @@ -58,17 +49,11 @@ 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= $(libdir)/pkgconfig | pkgconfigdir= $(prefix)/libdata/pkgconfig | ||||
- | |||||
-MKDIR_P = mkdir -p | -MKDIR_P = mkdir -p | ||||
-INSTALL = install -p | -INSTALL = install -p | ||||
-INSTALL_PROGRAM = $(INSTALL) | -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 | ||||
+pkgconfigdir= $(exec_prefix)/libdata/pkgconfig | - | ||||
# Set by config.mk if plugins are enabled | # Set by config.mk if plugins are enabled | ||||
plugindir = | plugindir = | ||||
@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \ | @@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \ | ||||
test/test-vcf-api \ | test/test-vcf-api \ | ||||
test/test-vcf-sweep | 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 | ||||
@@ -361,7 +346,7 @@ installdirs: | @@ -360,7 +345,7 @@ installdirs: | ||||
# and libhts.so.NN (used by client executables at runtime). | # and libhts.so.NN (used by client executables at runtime). | ||||
install-so: libhts.so installdirs | install-so: libhts.so installdirs | ||||
- $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) | - $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION) | ||||
+ $(INSTALL_LIB) 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 | ||||
ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) | ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION) | ||||