Hello Andreas & Udo, the project needed a few more patches (all attached).
Udo: I did not report these problems in the upstream github project, mainly because one has to fork the project and can not simply attach a patch to an issue. The patches: 01: silence some warnings that will become errors if C++11 should become the default with g++. 02: correct the initialization of minscore_ - it was initialized from itself. 03: unistd.h needs to be pulled in now manually. 04: Fixes the template scope problem Andreas actually asked about. 05: Updated Andreas the configure.ac/Makefile.am patch to properly link libprotobuf to the executables. It now compiles and links on my Debian testing machine - a few warnings are left though. I leave it to Andreas to merge the patches into the Debian scm - you can just replace the contents of debian/patches with the attached files. Best, Gert
Author: Gert Wollny <[email protected] 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 },
Author: Gert Wollny <[email protected] 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& ) ; } ;
Author: Gert Wollny <[email protected] 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 *
Author: Gert Wollny <[email protected] 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 )
Author: Andreas Tille <[email protected]>, Gert Wollny <[email protected] 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
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
