Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 27 May 2016 18:06:35 +0200
Description: Use Debian packaged libpcre

--- a/src/make-include.mk
+++ b/src/make-include.mk
@@ -57,7 +57,7 @@ else
 endif
 
 PHAST_VERSION=\"$(shell cat ${PHAST}/version)\"
-CFLAGS += -I${INC} -DPHAST_VERSION=${PHAST_VERSION} -DPHAST_HOME=\"${PHAST_HOME}\" -I${PHAST}/src/lib/pcre -fno-strict-aliasing
+CFLAGS += -I${INC} -DPHAST_VERSION=${PHAST_VERSION} -DPHAST_HOME=\"${PHAST_HOME}\" -fno-strict-aliasing
 LIBPATH = -L${LIB} 
 
 # uncomment these lines for profiling (add -g for line-by-line
@@ -138,8 +138,8 @@ else
 ifdef CLAPACKPATH
 ifneq ($(TARGETOS), Windows)
-  LIBS = -lphast -llapack -ltmglib -lblas -lc -lm
+  LIBS = -lphast -llapack -ltmglib -lblas -lc -lm -lpcre
 else
   CFLAGS += -I${CLAPACKPATH}/INCLUDE -I${F2CPATH} -DPCRE_STATIC
   LIBS = -lphast -lm  ${CLAPACKPATH}/liblapack.a ${CLAPACKPATH}/libf2c.a ${CLAPACKPATH}/libblas.a
 endif
 # IMPORTANT: use the following two lines instead for versions of CLAPACK
--- a/src/lib/Makefile
+++ b/src/lib/Makefile
@@ -3,7 +3,7 @@ PHAST := ${PHAST}/..
 
 CDIR = ${PWD}
 
-PACKAGES=base msa feature hmm phylo phylo_hmm motif pcre
+PACKAGES=base msa feature hmm phylo phylo_hmm motif
 
 ifdef RPHAST
 PACKAGES += rphast