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|
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}
|
