dev-lang/julia/files/julia-0.4.3-fix_build_system.patch

diff --git a/Make.inc b/Make.inc
index da01e38..c751607 100644
--- a/Make.inc
+++ b/Make.inc
@@ -297,7 +297,7 @@ JCFLAGS = -std=gnu99 -pipe $(fPIC) -fno-strict-aliasing -D_FILE_OFFSET_BITS=64
 JCPPFLAGS =
 JCXXFLAGS = -pipe $(fPIC) -fno-rtti
 DEBUGFLAGS = -O0 -ggdb3 -DJL_DEBUG_BUILD -fstack-protector-all
-SHIPFLAGS = -O3 -ggdb3 -falign-functions
+SHIPFLAGS = GENTOOCFLAGS
 endif
 
 ifeq ($(USECLANG),1)
@@ -307,7 +307,7 @@ JCFLAGS = -pipe $(fPIC) -fno-strict-aliasing -D_FILE_OFFSET_BITS=64
 JCPPFLAGS =
 JCXXFLAGS = -pipe $(fPIC) -fno-rtti
 DEBUGFLAGS = -O0 -g -DJL_DEBUG_BUILD -fstack-protector-all
-SHIPFLAGS = -O3 -g
+SHIPFLAGS =  GENTOOCFLAGS
 ifeq ($(OS), Darwin)
 ifeq ($(USE_LIBCPP), 1)
 CC += -stdlib=libc++ -mmacosx-version-min=10.7
@@ -334,7 +334,7 @@ JCFLAGS = -std=gnu11 -pipe $(fPIC) -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -
 JCPPFLAGS =
 JCXXFLAGS = -pipe $(fPIC) -fno-rtti
 DEBUGFLAGS = -O0 -g -DJL_DEBUG_BUILD -fstack-protector-all
-SHIPFLAGS = -O3 -g -falign-functions
+SHIPFLAGS = GENTOOCFLAGS
 endif
 
 ifeq ($(USECCACHE), 1)
diff --git a/deps/Makefile b/deps/Makefile
index 051b23d..881ba68 100644
--- a/deps/Makefile
+++ b/deps/Makefile
@@ -862,7 +862,7 @@ OPENSPECFUN_TAR_URL = https://api.github.com/repos/JuliaLang/openspecfun/tarball
 $(eval $(call git-external,openspecfun,OPENSPECFUN,Makefile,libopenspecfun.$(SHLIB_EXT)))
 
 # issue 8799
-OPENSPECFUN_CFLAGS = -O3 -std=c99
+OPENSPECFUN_CFLAGS = GENTOOCFLAGS -std=c99
 ifeq ($(USEICC),1)
   OPENSPECFUN_CFLAGS += -fp-model precise
 endif
@@ -902,7 +902,7 @@ DSFMT_OBJ_SOURCE = dsfmt-$(DSFMT_VER)/libdSFMT.$(SHLIB_EXT)
 
 DSFMT_CFLAGS = $(CFLAGS) -DNDEBUG -DDSFMT_MEXP=19937 $(fPIC) -DDSFMT_DO_NOT_USE_OLD_NAMES
 ifneq ($(USEMSVC), 1)
-DSFMT_CFLAGS += -O3 -finline-functions -fomit-frame-pointer -fno-strict-aliasing \
+DSFMT_CFLAGS += GENTOOCFLAGS -finline-functions -fno-strict-aliasing \
 		--param max-inline-insns-single=1800 -Wmissing-prototypes -Wall  -std=c99 -shared
 else
 DSFMT_CFLAGS += -Wl,-dll,-def:../libdSFMT.def
@@ -1181,7 +1181,7 @@ endif
 endif
 
 libgfortblas.$(SHLIB_EXT): gfortblas.c gfortblas.alias
-	$(CC) -Wall -O3 $(CPPFLAGS) $(CFLAGS) $(fPIC) -shared $< -o $@ -pipe \
+	$(CC) -Wall GENTOOCFLAGS $(CPPFLAGS) $(CFLAGS) $(fPIC) -shared $< -o $@ -pipe \
 				-Wl,-reexport_framework,Accelerate -Wl,-alias_list,gfortblas.alias
 $(build_shlibdir)/libgfortblas.$(SHLIB_EXT): libgfortblas.$(SHLIB_EXT)
 	cp -f $< $@
@@ -1607,10 +1607,10 @@ install-suitesparse: $(SUITESPARSE_OBJ_TARGET) install-suitesparse-wrapper
 # SUITESPARSE WRAPPER
 
 ifeq ($(USE_SYSTEM_SUITESPARSE), 1)
-SUITESPARSE_INC = -I /usr/include/suitesparse
+
 SUITESPARSE_LIB = -lumfpack -lcholmod -lamd -lcamd -lcolamd -lspqr
 else
-SUITESPARSE_INC = -I SuiteSparse-$(SUITESPARSE_VER)/CHOLMOD/Include -I SuiteSparse-$(SUITESPARSE_VER)/SuiteSparse_config -I SuiteSparse-$(SUITESPARSE_VER)/SPQR/Include
+
 SUITESPARSE_LIB = -L$(build_shlibdir) -lcholmod -lumfpack -lspqr $(RPATH_ORIGIN)
 $(build_shlibdir)/libsuitesparse_wrapper.$(SHLIB_EXT):  $(SUITESPARSE_OBJ_TARGET)
 endif
diff --git a/deps/checksums/Rmath-julia-0.1.tar.gz/sha512 b/deps/checksums/Rmath-julia-0.1.tar.gz/sha512
index 6a64d44..6bbeb34 100644
--- a/deps/checksums/Rmath-julia-0.1.tar.gz/sha512
+++ b/deps/checksums/Rmath-julia-0.1.tar.gz/sha512
@@ -1 +1 @@
-1dd94eca05bc06c3f33e8be5087d3b1742d01c8b38588e0fa79b8f6b9998760bca21bee1b65873825c4dde2d994a8271166bc21f670a34810fa9db598473a887
+15da0b3ff16113d5ad44c7ec42a1c8e260973883dd85ee174b3526f01137a94136cb03d4bbecb9267b7ca20d5ffc10670496d589cf60b86930f869a9fe219794
diff --git a/doc/Makefile b/doc/Makefile
index 08ba8dd..078d725 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -56,7 +56,7 @@ help:
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
 clean:
-	-rm -rf _build/*
+	@echo "Do not clean doc/_build/html. Just use it..."
 
 cleanall: clean
 
diff --git a/src/Makefile b/src/Makefile
index 98fa704..b566791 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -26,15 +26,8 @@ endif
 
 # In LLVM < 3.4, --ldflags includes both options and libraries, so use it both before and after --libs
 # In LLVM >= 3.4, --ldflags has only options, and --system-libs has the libraries.
-LLVMLINK = $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --libs) $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --system-libs 2> /dev/null)
-ifeq ($(USE_LLVM_SHLIB),1)
-ifeq ($(LLVM_USE_CMAKE),1)
-LLVMLINK = $(call exec,$(LLVM_CONFIG) --ldflags) -lLLVM
-else
-LLVMLINK = $(call exec,$(LLVM_CONFIG) --ldflags) -lLLVM-$(call exec,$(LLVM_CONFIG) --version)
-endif
+LLVMLINK = $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --libs) $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --system-libs)
 FLAGS += -DLLVM_SHLIB
-endif
 
 COMMON_LIBS = -L$(build_shlibdir) -L$(build_libdir) $(LIBUV) $(LIBUTF8PROC) $(NO_WHOLE_ARCHIVE) $(LLVMLINK) $(OSLIBS)
 DEBUG_LIBS = $(WHOLE_ARCHIVE) $(BUILDDIR)/flisp/libflisp-debug.a $(WHOLE_ARCHIVE) $(BUILDDIR)/support/libsupport-debug.a $(COMMON_LIBS)
diff --git a/ui/Makefile b/ui/Makefile
index c9b5d0e..557a38c 100644
--- a/ui/Makefile
+++ b/ui/Makefile
@@ -20,15 +20,10 @@ OBJS = $(SRCS:%=%.o)
 DOBJS = $(SRCS:%=%.dbg.obj)
 DEBUGFLAGS += $(FLAGS)
 SHIPFLAGS += $(FLAGS)
-ifeq ($(USE_LLVM_SHLIB),1)
-ifeq ($(LLVM_USE_CMAKE),1)
-LLVMLINK = $(call exec,$(LLVM_CONFIG) --ldflags) -lLLVM
-else
-LLVMLINK = $(call exec,$(LLVM_CONFIG) --ldflags) -lLLVM-$(call exec,$(LLVM_CONFIG) --version)
-endif
-else
-LLVMLINK =
-endif
+
+LLVMLINK = $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --libs) $(call exec,$(LLVM_CONFIG) --ldflags) $(call exec,$(LLVM_CONFIG) --system-libs)
+FLAGS += -DLLVM_SHLIB
+
 JLDFLAGS += $(LDFLAGS) $(NO_WHOLE_ARCHIVE) $(OSLIBS) $(LLVMLINK) $(RPATH)
 
 ifeq ($(USE_SYSTEM_LIBM),0)