[med-svn] [hmmer] 06/06: Try to use Debian packaged libdivsufsort but failed that way

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository hmmer.

commit 9d2b7a54d276c4cccc19593f2291843debac5cab
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 27 11:39:21 2016 +0200

    Try to use Debian packaged libdivsufsort but failed that way
---
 debian/patches/series                              |  1 +
 .../use_debian_packaged_libdivsufsort.patch        | 99 ++++++++++++++++++++++
 2 files changed, 100 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index 9075f02..79f6709 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 debian-changes-3.0-1
 debian-changes-3.0-2.1
+use_debian_packaged_libdivsufsort.patch
diff --git a/debian/patches/use_debian_packaged_libdivsufsort.patch b/debian/patches/use_debian_packaged_libdivsufsort.patch
new file mode 100644
index 0000000..99ed610
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libdivsufsort.patch
@@ -0,0 +1,99 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 26 Jun 2016 00:53:18 +0200
+Description: Use Debian packaged libdivsufsort
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -74,7 +74,6 @@ HMMER_LICENSE="Freely distributed under
+ HMMER_VERSION=$PACKAGE_VERSION
+ HMMER_URL="http://hmmer.org/"
+ HMMER_ESLDIR="easel"
+-HMMER_SADIR="libdivsufsort"
+ 
+ EASEL_DATE="February 2015"
+ EASEL_COPYRIGHT="Copyright (C) 2015 Howard Hughes Medical Institute."
+@@ -89,7 +88,6 @@ AC_SUBST(HMMER_LICENSE)
+ AC_SUBST(HMMER_VERSION)
+ AC_SUBST(HMMER_URL)
+ AC_SUBST(HMMER_ESLDIR)
+-AC_SUBST(HMMER_SADIR)
+ 
+ AC_SUBST(EASEL_DATE)
+ AC_SUBST(EASEL_COPYRIGHT)
+@@ -669,14 +667,12 @@ AC_CONFIG_FILES([profmark/Makefile])
+ AC_CONFIG_FILES([src/impl_${impl_choice}/Makefile])
+ AC_CONFIG_HEADERS([src/p7_config.h])
+ AC_CONFIG_HEADERS([easel/esl_config.h])
+-AC_CONFIG_HEADERS([libdivsufsort/divsufsort.h])
+ AC_CONFIG_FILES([easel/miniapps/Makefile])
+ AC_CONFIG_FILES([easel/testsuite/Makefile])
+ if test -d "easel/documentation"; then
+   AC_CONFIG_FILES([easel/documentation/Makefile])
+ fi    
+ AC_CONFIG_FILES([easel/Makefile])
+-AC_CONFIG_FILES([libdivsufsort/Makefile])
+ 
+ # the following incantation establishes a symlink of
+ # src/impl_{whatever} to src/impl in the *build* directory.
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -24,8 +24,6 @@ SHELL          = /bin/sh
+ # location of easel
+ ESLDIR         = @HMMER_ESLDIR@
+ 
+-# location of libdivsufsort for suffix array creation
+-SADIR          = @HMMER_SADIR@
+ 
+ 
+ # Package information
+@@ -102,7 +100,6 @@ PROGS = alimask\
+ #
+ 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
+ 
+@@ -110,7 +107,6 @@ all:
+ #
+ 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
+ 
+@@ -124,7 +120,6 @@ tests:
+ #
+ check:
+ 	${QUIET_SUBDIR0}${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
+@@ -162,7 +157,6 @@ clean:
+ 	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} clean
+ 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
+ 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} clean
+-	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} clean
+ 	-rm -f *.o *~ Makefile.bak core TAGS gmon.out
+ 
+ # "make distclean" leaves a pristine source distribution.
+@@ -173,7 +167,6 @@ distclean:
+ 	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} distclean
+ 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
+ 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} distclean
+-	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} distclean
+ 	-rm config.log config.status
+ 	-rm -rf autom4te.cache
+ 	-rm -f *.o *~ Makefile.bak core TAGS gmon.out
+@@ -223,10 +216,6 @@ tags-append:
+ 	etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/userguide/*.in
+ 	etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/userguide/*.tex
+ 
+-	etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/README
+-	etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/*.in
+-	etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/*.c
+-
+ 	etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/00README
+ 	etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/*.in
+ 	etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/*.c

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