[med-svn] r15729 - trunk/packages/anfo/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Wed Jan 8 12:16:22 UTC 2014
Author: tille
Date: 2014-01-08 12:16:22 +0000 (Wed, 08 Jan 2014)
New Revision: 15729
Added:
trunk/packages/anfo/trunk/debian/patches/01-silence-narrowing-conversion.patch
trunk/packages/anfo/trunk/debian/patches/02-correct-minscore-self-initialization.patch
trunk/packages/anfo/trunk/debian/patches/03-include-unistd-forF_OK.patch
trunk/packages/anfo/trunk/debian/patches/04-reorder-template-for-new-scope-rules.patch
trunk/packages/anfo/trunk/debian/patches/05-autoreconf.patch
Removed:
trunk/packages/anfo/trunk/debian/patches/autoreconf.patch
Modified:
trunk/packages/anfo/trunk/debian/patches/series
Log:
Inject patches created by Gert Wollny (thanks a lot!)
Added: trunk/packages/anfo/trunk/debian/patches/01-silence-narrowing-conversion.patch
===================================================================
--- trunk/packages/anfo/trunk/debian/patches/01-silence-narrowing-conversion.patch (rev 0)
+++ trunk/packages/anfo/trunk/debian/patches/01-silence-narrowing-conversion.patch 2014-01-08 12:16:22 UTC (rev 15729)
@@ -0,0 +1,19 @@
+Author: Gert Wollny <gw.fossdev at gmail.com
+Last-Update: Wed, 08 Jan 2014 11:55:33 +0100
+Description: Force initialization to unsigned because the conversion is narrowing
+ Here this is still only a warning but with C++11 this will be an error.
+
+diff -ur -x Makefile.in anfo-0.98/src/anfo-tool.cc anfo-0.98.debian/src/anfo-tool.cc
+--- anfo-0.98/src/anfo-tool.cc 2010-09-24 14:18:59.000000000 +0200
++++ anfo-0.98.debian/src/anfo-tool.cc 2014-01-08 11:37:35.884269960 +0100
+@@ -461,8 +461,8 @@
+ { "output-wiggle", 0 , POPT_ARG_STRING, 0, opt_output_wiggle, "write depth-of-coverage in WIG format to FILE", "FILE" },
+ { "duct-tape", 0 , POPT_ARG_STRING, 0, opt_duct_tape, "mock-assemble into contigs named NAME", "NAME" },
+
+- { "set-slope", 0 , POPT_ARG_DFLT, ¶m.slope, 0, "set slope parameter to S", "S" },
+- { "set-intercept", 0 , POPT_ARG_DFLT, ¶m.intercept, 0, "set length discount parameter to L", "L" },
++ { "set-slope", 0 , (unsigned)POPT_ARG_DFLT, ¶m.slope, 0, "set slope parameter to S", "S" },
++ { "set-intercept", 0 , (unsigned)POPT_ARG_DFLT, ¶m.intercept, 0, "set length discount parameter to L", "L" },
+ { "set-genome", 0 , POPT_ARG_STRING, ¶m.genome, 0, "set interesting genome parameter to G", "G" },
+ { "clear-genome", 0 , POPT_ARG_VAL, ¶m.genome, 0, "clear interesting genome parameter", 0 },
+
Added: trunk/packages/anfo/trunk/debian/patches/02-correct-minscore-self-initialization.patch
===================================================================
--- trunk/packages/anfo/trunk/debian/patches/02-correct-minscore-self-initialization.patch (rev 0)
+++ trunk/packages/anfo/trunk/debian/patches/02-correct-minscore-self-initialization.patch 2014-01-08 12:16:22 UTC (rev 15729)
@@ -0,0 +1,16 @@
+Author: Gert Wollny <gw.fossdev at gmail.com
+Last-Update: Wed, 08 Jan 2014 11:55:33 +0100
+Description: Correct initialization of minscore_
+
+diff -ur -x Makefile.in anfo-0.98/src/anfo_common.h anfo-0.98.debian/src/anfo_common.h
+--- anfo-0.98/src/anfo_common.h 2010-09-24 14:19:00.000000000 +0200
++++ anfo-0.98.debian/src/anfo_common.h 2014-01-08 11:33:26.118447741 +0100
+@@ -66,7 +66,7 @@
+ {}
+
+ Housekeeper( vector<string> left, vector<string> right, int minscore )
+- : minscore_( minscore_ ), trim_left_( left ), trim_right_( right ) {}
++ : minscore_( minscore ), trim_left_( left ), trim_right_( right ) {}
+
+ virtual void put_result( const Result& ) ;
+ } ;
Added: trunk/packages/anfo/trunk/debian/patches/03-include-unistd-forF_OK.patch
===================================================================
--- trunk/packages/anfo/trunk/debian/patches/03-include-unistd-forF_OK.patch (rev 0)
+++ trunk/packages/anfo/trunk/debian/patches/03-include-unistd-forF_OK.patch 2014-01-08 12:16:22 UTC (rev 15729)
@@ -0,0 +1,15 @@
+Author: Gert Wollny <gw.fossdev at gmail.com
+Last-Update: Wed, 08 Jan 2014 11:55:33 +0100
+Description: Include unistd.h to make F_OK available
+
+diff -ur -x Makefile.in anfo-0.98/src/conffile.h anfo-0.98.debian/src/conffile.h
+--- anfo-0.98/src/conffile.h 2010-09-24 14:15:00.000000000 +0200
++++ anfo-0.98.debian/src/conffile.h 2014-01-08 11:35:28.621379698 +0100
+@@ -22,6 +22,7 @@
+ #include <google/protobuf/text_format.h>
+ #include <fstream>
+ #include <string>
++#include <unistd.h>
+
+ /*! \page configuration Configuration Files, Metadata, Output Format
+ *
Added: trunk/packages/anfo/trunk/debian/patches/04-reorder-template-for-new-scope-rules.patch
===================================================================
--- trunk/packages/anfo/trunk/debian/patches/04-reorder-template-for-new-scope-rules.patch (rev 0)
+++ trunk/packages/anfo/trunk/debian/patches/04-reorder-template-for-new-scope-rules.patch 2014-01-08 12:16:22 UTC (rev 15729)
@@ -0,0 +1,56 @@
+Author: Gert Wollny <gw.fossdev at gmail.com
+Last-Update: Wed, 08 Jan 2014 11:55:33 +0100
+Description: Correct ordering of template declarations to honor new scope rules
+
+diff -ur -x Makefile.in anfo-0.98/src/stream.h anfo-0.98.debian/src/stream.h
+--- anfo-0.98/src/stream.h 2010-09-24 14:19:00.000000000 +0200
++++ anfo-0.98.debian/src/stream.h 2014-01-08 11:34:01.542138919 +0100
+@@ -141,6 +141,9 @@
+ output::Hit* mutable_hit_to( output::Result* ) ;
+ output::Hit* mutable_hit_to( output::Result*, const string& ) ;
+
++inline output::Hit::Operation cigar_op( uint32_t c ) { return (output::Hit::Operation)(c & 0xf) ; }
++inline uint32_t cigar_len( uint32_t c ) { return c >> 4 ; }
++
+ //! \brief computes (trimmed) query length from CIGAR line
+ template< typename C > unsigned len_from_bin_cigar( const C& cig )
+ {
+@@ -166,8 +169,6 @@
+ return l ;
+ }
+
+-inline output::Hit::Operation cigar_op( uint32_t c ) { return (output::Hit::Operation)(c & 0xf) ; }
+-inline uint32_t cigar_len( uint32_t c ) { return c >> 4 ; }
+ inline uint32_t mk_cigar( output::Hit::Operation op, uint32_t len ) { return len << 4 | op ; }
+
+ inline void push_op( std::vector<unsigned>& s, unsigned m, output::Hit::Operation op )
+diff -ur -x Makefile.in anfo-0.98/src/util.h anfo-0.98.debian/src/util.h
+--- anfo-0.98/src/util.h 2010-09-24 14:19:00.000000000 +0200
++++ anfo-0.98.debian/src/util.h 2014-01-08 11:30:42.819871162 +0100
+@@ -44,6 +44,13 @@
+ }
+
+ template< typename T >
++T throw_errno_if_eq( T x, T y, const char* a, const char* b = 0 )
++{
++ if( x == y ) throw_errno( a, b ) ;
++ return x ;
++}
++
++template< typename T >
+ T throw_errno_if_minus1( T x, const char* a, const char* b = 0 )
+ { return throw_errno_if_eq( x, (T)(-1), a, b ) ; }
+
+@@ -51,12 +58,6 @@
+ T throw_errno_if_null( T x, const char* a, const char* b = 0 )
+ { return throw_errno_if_eq( x, (T)0, a, b ) ; }
+
+-template< typename T >
+-T throw_errno_if_eq( T x, T y, const char* a, const char* b = 0 )
+-{
+- if( x == y ) throw_errno( a, b ) ;
+- return x ;
+-}
+
+ template< typename T >
+ T throw_if_negative( T x, const char* a, const char* b = 0 )
Added: trunk/packages/anfo/trunk/debian/patches/05-autoreconf.patch
===================================================================
--- trunk/packages/anfo/trunk/debian/patches/05-autoreconf.patch (rev 0)
+++ trunk/packages/anfo/trunk/debian/patches/05-autoreconf.patch 2014-01-08 12:16:22 UTC (rev 15729)
@@ -0,0 +1,42 @@
+Author: Andreas Tille <tille at debian.org>, Gert Wollny <gw.fossdev at gmail.com
+Last-Update: Wed, 08 Jan 2014 11:55:33 +0100
+Description: Enable using autoreconf and add protobuf to global link command
+
+diff -ur -x Makefile.in anfo-0.98/src/Makefile.am anfo-0.98.debian/src/Makefile.am
+--- anfo-0.98/src/Makefile.am 2010-09-24 16:00:06.000000000 +0200
++++ anfo-0.98.debian/src/Makefile.am 2014-01-08 11:44:35.008758531 +0100
+@@ -15,9 +15,9 @@
+ BUILT_SOURCES = config.pb.h output.pb.h config.pb.cc output.pb.cc
+ CLEANFILES = config.pb.h output.pb.h config.pb.cc output.pb.cc anfo.scm
+
+-CFLAGS += $(protobuf_CFLAGS)
+-CXXFLAGS += $(protobuf_CFLAGS)
+-LDADD = libanfo.la
++AM_CFLAGS = $(protobuf_CFLAGS)
++AM_CXXFLAGS = $(protobuf_CFLAGS)
++LDADD = libanfo.la $(protobuf_LIBS)
+
+ libanfo_la_LDFLAGS = -version-info 0:0:0
+ libanfo_la_LIBADD = $(protobuf_LIBS) -lpthread
+@@ -40,10 +40,10 @@
+ sed -e "s#__LIBDIR__#$(libdir)#g" < $(srcdir)/anfo.scm.in >> anfo.scm
+
+ config.pb.cc: config.proto
+- $(PROTOC) -I. -I$(dir $(PROTOC))../include --cpp_out=. config.proto
++ protoc -I. -I/usr/include --cpp_out=. config.proto
+
+ output.pb.cc: output.proto
+- $(PROTOC) -I. -I$(dir $(PROTOC))../include --cpp_out=. output.proto
++ protoc -I. -I/usr/include --cpp_out=. output.proto
+
+ config.pb.h: config.pb.cc
+ @:
+--- anfo-0.98.orig/configure.ac
++++ anfo-0.98/configure.ac
+@@ -72,3 +72,6 @@
+ src/Makefile
+ ])
+ AC_OUTPUT
++
++m4_pattern_allow([AM_PROG_AR])
++AM_PROG_AR
Deleted: trunk/packages/anfo/trunk/debian/patches/autoreconf.patch
===================================================================
--- trunk/packages/anfo/trunk/debian/patches/autoreconf.patch 2014-01-06 12:29:15 UTC (rev 15728)
+++ trunk/packages/anfo/trunk/debian/patches/autoreconf.patch 2014-01-08 12:16:22 UTC (rev 15729)
@@ -1,39 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 01 Jan 2014 17:55:33 +0100
-Description: Enable using autoreconf
-
---- anfo-0.98.orig/src/Makefile.am
-+++ anfo-0.98/src/Makefile.am
-@@ -15,8 +15,8 @@
- BUILT_SOURCES = config.pb.h output.pb.h config.pb.cc output.pb.cc
- CLEANFILES = config.pb.h output.pb.h config.pb.cc output.pb.cc anfo.scm
-
--CFLAGS += $(protobuf_CFLAGS)
--CXXFLAGS += $(protobuf_CFLAGS)
-+AM_CFLAGS = $(protobuf_CFLAGS)
-+AM_CXXFLAGS = $(protobuf_CFLAGS)
- LDADD = libanfo.la
-
- libanfo_la_LDFLAGS = -version-info 0:0:0
-@@ -40,10 +40,10 @@
- sed -e "s#__LIBDIR__#$(libdir)#g" < $(srcdir)/anfo.scm.in >> anfo.scm
-
- config.pb.cc: config.proto
-- $(PROTOC) -I. -I$(dir $(PROTOC))../include --cpp_out=. config.proto
-+ protoc -I. -I/usr/include --cpp_out=. config.proto
-
- output.pb.cc: output.proto
-- $(PROTOC) -I. -I$(dir $(PROTOC))../include --cpp_out=. output.proto
-+ protoc -I. -I/usr/include --cpp_out=. output.proto
-
- config.pb.h: config.pb.cc
- @:
---- anfo-0.98.orig/configure.ac
-+++ anfo-0.98/configure.ac
-@@ -72,3 +72,6 @@
- src/Makefile
- ])
- AC_OUTPUT
-+
-+m4_pattern_allow([AM_PROG_AR])
-+AM_PROG_AR
Modified: trunk/packages/anfo/trunk/debian/patches/series
===================================================================
--- trunk/packages/anfo/trunk/debian/patches/series 2014-01-06 12:29:15 UTC (rev 15728)
+++ trunk/packages/anfo/trunk/debian/patches/series 2014-01-08 12:16:22 UTC (rev 15729)
@@ -1 +1,5 @@
-autoreconf.patch
+01-silence-narrowing-conversion.patch
+02-correct-minscore-self-initialization.patch
+03-include-unistd-forF_OK.patch
+04-reorder-template-for-new-scope-rules.patch
+05-autoreconf.patch
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