[med-svn] [hmmer2] 09/09: Fix build against Debian packaged libsquid

[Andreas Tille]

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tille pushed a commit to branch master
in repository hmmer2.

commit e83b165d30673e35fbcb2506ab0f81c10de007eb
Author: Andreas Tille <tille at debian.org>
Date:   Wed Apr 12 13:17:57 2017 +0200

    Fix build against Debian packaged libsquid
---
 debian/patches/use_debian_packaged_biosquid.patch | 61 +++++++++++++++++++++--
 1 file changed, 58 insertions(+), 3 deletions(-)

diff --git a/debian/patches/use_debian_packaged_biosquid.patch b/debian/patches/use_debian_packaged_biosquid.patch
index 5536f7f..d6ee42f 100644
--- a/debian/patches/use_debian_packaged_biosquid.patch
+++ b/debian/patches/use_debian_packaged_biosquid.patch
@@ -1,3 +1,8 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 11 Apr 2017 17:24:13 +0200
+Description: Link against Debian packaged libsquid and remove
+ duplicated functions from there
+
 --- a/src/Makefile.in
 +++ b/src/Makefile.in
 @@ -42,9 +42,9 @@ PVMLIBS   = @PVMLIBS@
@@ -77,7 +82,12 @@
   * 
 --- a/configure
 +++ b/configure
-@@ -2601,7 +2601,7 @@ echo "$as_me: configured for optional LF
+@@ -2597,11 +2597,11 @@ if test "${enable_lfs+set}" = set; then
+    yes) { echo "$as_me:$LINENO: configured for optional LFS, large file support" >&5
+ echo "$as_me: configured for optional LFS, large file support" >&6;}
+ 	cat >>confdefs.h <<\_ACEOF
+-#define _LARGEFILE_SOURCE 1
++#define _LARGEFILE_SOURCE_defined_in_biosquid 1
  _ACEOF
  
  	cat >>confdefs.h <<\_ACEOF
@@ -88,11 +98,56 @@
  	cat >>confdefs.h <<\_ACEOF
 --- a/src/config.h.in
 +++ b/src/config.h.in
-@@ -97,7 +97,6 @@
+@@ -96,8 +96,6 @@
+ 
  /* --enable-lfs          Large File Summit (LFS) support for >2Gb files
   */
- #undef _LARGEFILE_SOURCE
+-#undef _LARGEFILE_SOURCE
 -#undef _LARGEFILE64_SOURCE
  #undef _FILE_OFFSET_BITS
  
  /* --enable-pvm          Parallel Virtual Machine (PVM)
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -87,7 +87,6 @@ all:
+ 	  echo "If you really want to rebuild from source, move or delete the" ;\
+ 	  echo "binaries/ subdirectory."; \
+ 	else\
+-	  (cd squid;     ${MAKE}; ${MAKE} module);\
+ 	  (cd src;       ${MAKE}; ${MAKE} module);\
+ 	  (cd testsuite; ${MAKE});\
+ 	fi
+@@ -98,9 +97,6 @@ all:
+ check:	
+ 	(cd testsuite; make check)
+ 
+-squid/libsquid.a:
+-	(cd squid; make; make module)
+-
+ src/libhmmer.a: 
+ 	(cd src;   make; make module)
+ 
+@@ -143,7 +139,6 @@ bindist:
+ #
+ clean:
+ 	(cd src;       make clean)
+-	(cd squid;     make clean)
+ 	(cd testsuite; make clean)
+ 	-rm -f *.o *~ Makefile.bak core TAGS gmon.out
+ 
+@@ -156,7 +151,6 @@ distclean:
+ 	-rm -f *.o *~ Makefile.bak core TAGS gmon.out
+ 	-rm Makefile
+ 	(cd src;       make distclean)
+-	(cd squid;     make distclean)
+ 	(cd testsuite; make distclean)
+ 
+ 
+@@ -165,7 +159,6 @@ distclean:
+ #
+ binclean:
+ 	(cd src;       make binclean)
+-	(cd squid;     make binclean)
+ 	(cd testsuite; make binclean)
+ 	-rm -f *.o *~ Makefile.bak core TAGS gmon.out
+ 	-rm config.log config.status

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