Author: Andreas Tille <tille@debian.org>
Last-Update: Sun, 26 Jun 2016 00:53:18 +0200
Description: Use Debian packaged libdivsufsort
Forwarded: not-needed
--- hmmer.orig/configure.ac
+++ hmmer/configure.ac
@@ -114,7 +114,6 @@
 HMMER_URL="http://hmmer.org/"
 
 HMMER_ESLDIR="easel"
-HMMER_SADIR="libdivsufsort"
 
 EASEL_DATE="Nov 2020"
 EASEL_COPYRIGHT="Copyright (C) 2020 Howard Hughes Medical Institute."
@@ -129,7 +128,6 @@
 AC_SUBST(HMMER_URL)
 
 AC_SUBST(HMMER_ESLDIR)
-AC_SUBST(HMMER_SADIR)
 
 AC_SUBST(EASEL_DATE)
 AC_SUBST(EASEL_COPYRIGHT)
@@ -587,7 +585,6 @@
   documentation/man/Makefile                   \
   documentation/userguide/Makefile             \
   documentation/userguide/inclusions/Makefile  \
-  libdivsufsort/Makefile                       \
   ])
 
 # Easel Makefiles.
@@ -663,7 +660,6 @@
 AC_CONFIG_HEADERS([easel/decoy_config.h])   # Put this first to keep gnu 'autoheader' from overwriting a real config file.
 AC_CONFIG_HEADERS([src/p7_config.h])
 AC_CONFIG_HEADERS([easel/esl_config.h])
-AC_CONFIG_HEADERS([libdivsufsort/divsufsort.h])
 
 # the following incantation establishes a symlink of
 # src/impl_{whatever} to src/impl in the *build* directory.
--- hmmer.orig/Makefile.in
+++ hmmer/Makefile.in
@@ -26,8 +26,6 @@
 # location of easel
 ESLDIR         = @HMMER_ESLDIR@
 
-# location of libdivsufsort for suffix array creation
-SADIR          = @HMMER_SADIR@
 
 
 # Package information
@@ -88,7 +86,6 @@
 #
 all: 
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} all
-	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}profmark      ${QUIET_SUBDIR1} all
 
@@ -96,7 +93,6 @@
 #
 dev: 
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} dev
-	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} dev
 	${QUIET_SUBDIR0}profmark   ${QUIET_SUBDIR1} dev
 
@@ -111,7 +107,6 @@
 check:
 	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make check', but is not in your PATH. Aborting."; exit 1; }
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} tests
-	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all	
 	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} tests
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} check
 	${QUIET_SUBDIR0}testsuite  ${QUIET_SUBDIR1} check
@@ -157,7 +152,6 @@
 	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} clean
 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} clean
-	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} clean
 	${QUIET}-rm -f *.o *~ Makefile.bak core TAGS TAGS.part gmon.out
 ifndef V
 	@echo '     ' CLEAN hmmer
@@ -171,7 +165,6 @@
 	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} distclean
 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} distclean
-	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} distclean
 	${QUIET}-rm config.log config.status
 	${QUIET}-rm -rf autom4te.cache
 	${QUIET}-rm -f *.o *~ Makefile.bak core TAGS TAGS.part gmon.out
--- hmmer.orig/src/Makefile.in
+++ hmmer/src/Makefile.in
@@ -37,11 +37,9 @@
 
 IMPLDIR   = impl_@IMPL_CHOICE@
 ESLDIR    = @HMMER_ESLDIR@
-SADIR     = @HMMER_SADIR@
 
-MYLIBDIRS = -L../${ESLDIR} -L./${IMPLDIR} -L../${SADIR} -L.
+MYLIBDIRS = -L../${ESLDIR} -L./${IMPLDIR} -L.
 MYINCDIRS = -I../${ESLDIR} \
-	    -I../${SADIR} \
 	    -I${top_srcdir}/easel \
 	    -I. \
 	    -I${srcdir}
