diff options
| author | Ethan Morgan <ethan@gweithio.com> | 2026-02-14 16:44:06 +0000 |
|---|---|---|
| committer | Ethan Morgan <ethan@gweithio.com> | 2026-02-14 16:44:06 +0000 |
| commit | 54409423f767d8b1cf30cb7d0efca6b4ca138823 (patch) | |
| tree | d915ac7828703ce4b963efdd9728a1777ba18c1e /vcpkg/ports/htslib/0002-pthread-flag.patch | |
Diffstat (limited to 'vcpkg/ports/htslib/0002-pthread-flag.patch')
| -rw-r--r-- | vcpkg/ports/htslib/0002-pthread-flag.patch | 78 |
1 files changed, 78 insertions, 0 deletions
diff --git a/vcpkg/ports/htslib/0002-pthread-flag.patch b/vcpkg/ports/htslib/0002-pthread-flag.patch new file mode 100644 index 0000000..d94dd0a --- /dev/null +++ b/vcpkg/ports/htslib/0002-pthread-flag.patch @@ -0,0 +1,78 @@ +diff --git a/Makefile b/Makefile +index e98f287..ab3fdc1 100644 +--- a/Makefile ++++ b/Makefile +@@ -145,6 +145,8 @@ HTS_BUILD_AVX2 = + HTS_BUILD_AVX512 = + HTS_BUILD_SSE4 = + ++PTHREAD = -pthread ++ + include htslib_vars.mk + include htscodecs.mk + +@@ -191,10 +193,10 @@ config_vars.h: + .SUFFIXES: .bundle .c .cygdll .dll .o .pico .so + + .c.o: +- $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< ++ $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(PTHREAD) -c -o $@ $< + + .c.pico: +- $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $< ++ $(CC) $(CFLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) $(PTHREAD) $(EXTRA_CFLAGS_PIC) -c -o $@ $< + + ref_cache/%.o: ref_cache/%.c + $(CC) $(CFLAGS) $(REF_CACHE_EXTRA_C_FLAGS) $(TARGET_CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $< +@@ -409,7 +411,7 @@ print-config: + # file used at runtime (when $LD_LIBRARY_PATH includes the build directory). + + libhts.so: $(LIBHTS_OBJS:.o=.pico) +- $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(VERSION_SCRIPT_LDFLAGS) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) -lpthread ++ $(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(VERSION_SCRIPT_LDFLAGS) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) $(PTHREAD) + ln -sf $@ libhts.so.$(LIBHTS_SOVERSION) + + # Similarly this also creates libhts.NN.dylib as a byproduct, so that programs +@@ -421,10 +423,10 @@ libhts.dylib: $(LIBHTS_OBJS) + ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib + + cyghts-$(LIBHTS_SOVERSION).dll libhts.dll.a: $(LIBHTS_OBJS) +- $(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread ++ $(CC) -shared -Wl,--out-implib=libhts.dll.a -Wl,--enable-auto-import $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) $(PTHREAD) + + hts-$(LIBHTS_SOVERSION).dll hts.dll.a: $(LIBHTS_OBJS) +- $(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) -lpthread ++ $(CC) -shared -Wl,--out-implib=hts.dll.a -Wl,--enable-auto-import -Wl,--exclude-all-symbols $(LDFLAGS) -o $@ -Wl,--whole-archive $(LIBHTS_OBJS) -Wl,--no-whole-archive $(LIBS) $(PTHREAD) + + hts-$(LIBHTS_SOVERSION).def: hts-$(LIBHTS_SOVERSION).dll + gendef hts-$(LIBHTS_SOVERSION).dll +@@ -471,7 +473,7 @@ hts-object-files: $(LIBHTS_OBJS) + # may not be able to access libhts symbols via the main program's libhts + # if that was dynamically loaded without an explicit RTLD_GLOBAL. + %.so: %.pico libhts.so +- $(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< libhts.so $(LIBS) -lpthread ++ $(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< libhts.so $(LIBS) $(PTHREAD) + + # For programs *statically* linked to libhts.a, on macOS loading a plugin + # linked to a shared libhts.NN.dylib would lead to conflicting duplicate +@@ -553,16 +555,16 @@ htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static3 + htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico: TARGET_CFLAGS = $(HTS_CFLAGS_SSE4) + + annot-tsv: annot-tsv.o libhts.a +- $(CC) $(LDFLAGS) -o $@ annot-tsv.o libhts.a $(LIBS) -lpthread ++ $(CC) $(LDFLAGS) -o $@ annot-tsv.o libhts.a $(LIBS) $(PTHREAD) + + bgzip: bgzip.o libhts.a +- $(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) -lpthread ++ $(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) $(PTHREAD) + + htsfile: htsfile.o libhts.a +- $(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) -lpthread ++ $(CC) $(LDFLAGS) -o $@ htsfile.o libhts.a $(LIBS) $(PTHREAD) + + tabix: tabix.o libhts.a +- $(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread ++ $(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) $(PTHREAD) + + ref_cache/ref-cache: $(REF_CACHE_OBJS) + $(CC) $(LDFLAGS) $(REF_CACHE_EXTRA_LD_FLAGS) -o $@ $(REF_CACHE_OBJS) -lcurl |