[med-svn] [Git][med-team/ksw2][master] 2 commits: propagate HAVE_KALLOC with presence of kalloc.h

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / ksw2


Commits:
f42f8009 by Etienne Mollier at 2020-07-10T23:58:59+02:00
propagate HAVE_KALLOC with presence of kalloc.h

- - - - -
da418f92 by Etienne Mollier at 2020-07-11T01:05:46+02:00
check and use parasail from /usr/include

- - - - -


2 changed files:

- debian/control
- debian/patches/autoconf.patch


Changes:

=====================================
debian/control
=====================================
@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 12),
                autoconf-archive,
                pkg-config,
                zlib1g-dev,
+               libparasail-dev,
                libsimde-dev
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/ksw2


=====================================
debian/patches/autoconf.patch
=====================================
@@ -3,7 +3,7 @@ Last-Update: Fri, 15 May 2020 11:45:35 +0200
 Description: Provide automake build system to get proper library packaging
 
 --- /dev/null
-+++ b/Makefile.am
++++ ksw2/Makefile.am
 @@ -0,0 +1,19 @@
 +lib_LTLIBRARIES  = libksw2.la
 +
@@ -25,7 +25,7 @@ Description: Provide automake build system to get proper library packaging
 +
 +
 --- /dev/null
-+++ b/configure.ac
++++ ksw2/configure.ac
 @@ -0,0 +1,66 @@
 +#                                               -*- Autoconf -*-
 +# Process this file with autoconf to produce a configure script.
@@ -80,11 +80,11 @@ Description: Provide automake build system to get proper library packaging
 +# Checks for header files.
 +AC_HEADER_STDC
 +AC_CHECK_HEADERS([stdlib.h])
++AC_CHECK_HEADERS([parasail.h],[AC_DEFINE([HAVE_PARASAIL], [1], [Use parasail])])
 +
 +AC_PROG_MAKE_SET
 +
-+dnl AC_DEFINE([HAVE_KALLOC], [1], [Use ksw2 own malloc functions])
-+AC_CHECK_HEADER([kalloc.h], [AC_DEFINE([HAVE_KALLOC], [1], [Use ksw2 own malloc functions])] )
++AC_CHECK_FILE([kalloc.h],[AC_DEFINE([HAVE_KALLOC], [1], [Use ksw2 own malloc functions])])
 +
 +AC_CONFIG_FILES([
 +	Makefile
@@ -94,7 +94,7 @@ Description: Provide automake build system to get proper library packaging
 +
 +
 --- /dev/null
-+++ b/libksw2.pc.in
++++ ksw2/libksw2.pc.in
 @@ -0,0 +1,12 @@
 +prefix=@prefix@
 +exec_prefix=${prefix}
@@ -108,7 +108,7 @@ Description: Provide automake build system to get proper library packaging
 +Libs: -L${libdir} -lksw2
 +Cflags: -I${includedir}
 +
---- a/Makefile
+--- ksw2.orig/Makefile
 +++ /dev/null
 @@ -1,58 +0,0 @@
 -CC=			gcc
@@ -169,3 +169,14 @@ Description: Provide automake build system to get proper library packaging
 -ksw2_gg.o: ksw2.h
 -ksw2_gg2.o: ksw2.h
 -ksw2_gg2_sse.o: ksw2.h
+--- ksw2.orig/cli.c
++++ ksw2/cli.c
+@@ -11,7 +11,7 @@
+ #endif
+ 
+ #ifdef HAVE_PARASAIL
+-#include "parasail.h"
++#include <parasail.h>
+ #endif
+ 
+ unsigned char seq_nt4_table[256] = {



View it on GitLab: https://salsa.debian.org/med-team/ksw2/-/compare/1dff0e6b3018d1a26563c2e0666c97ac91df518d...da418f92e8e51907fc61ca1655f68db0dcdccc4b

-- 
View it on GitLab: https://salsa.debian.org/med-team/ksw2/-/compare/1dff0e6b3018d1a26563c2e0666c97ac91df518d...da418f92e8e51907fc61ca1655f68db0dcdccc4b
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