/[gentoo-x86]/sci-biology/allpaths/files/allpaths-3.1-boost-1.50-2.patch
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Contents of /sci-biology/allpaths/files/allpaths-3.1-boost-1.50-2.patch

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Revision 1.1 - (hide annotations) (download)
Thu Nov 8 20:54:22 2012 UTC (4 years, 11 months ago) by jlec
Branch: MAIN
sci-biology/allpaths: Fix for latest boost, #421727; fix for additional problem with gcc-4.7; enable openmp support; Respect LDFALGS and CFLAGS everywhere; make it gold resistant

(Portage version: 2.2.0_alpha142/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

1 jlec 1.1 MakeDepend.cc | 9 +++++----
2     Makefile.in | 12 ++++++------
3     Makefile_g++ | 3 ++-
4     TestProgram.cc | 1 +
5     lookup/CreateLookupTab.cc | 3 +++
6     paths/AlignPairsToHyper3G.cc | 2 ++
7     paths/ErrorCorrectJump.cc | 2 ++
8     reporting/FastbStats.cc | 1 +
9     util/FastaParser.cc | 3 +++
10     9 files changed, 25 insertions(+), 11 deletions(-)
11    
12     diff --git a/MakeDepend.cc b/MakeDepend.cc
13     index 619e6f7..b8d9c72 100644
14     --- a/MakeDepend.cc
15     +++ b/MakeDepend.cc
16     @@ -1032,7 +1032,7 @@ void makefile_builder::GenerateMakefileForSharedLibs( ostream &mf )
17     mf << " " << dep_iter->Provider();
18     mf << "\n";
19     mf << "\t" << "mkdir -p $(LIB)" << endl;
20     - mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) -o $(LIB)/" << *lib_iter;
21     + mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) $(L_FLAGS) -o $(LIB)/" << *lib_iter;
22     for ( vector<dependency>::iterator dep_iter = link_deps.first;
23     dep_iter != link_deps.second; ++dep_iter )
24     mf << " $(OBJ)/" << dep_iter->Provider();
25     @@ -1182,7 +1182,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
26     mf << " $(OBJ)/" << *dep_iter;
27     }
28     mf << "\n\t$(BIN)/checkLock $(BIN)/$@";
29     - mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ ";
30     + mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) $(L_FLAGS) -o $(BIN)/$@ ";
31     for ( set<string>::iterator dep_iter = obj_deps.begin();
32     dep_iter != obj_deps.end(); ++dep_iter )
33     {
34     @@ -1195,7 +1195,8 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
35     mf << " $(OBJ)/" << *dep_iter;
36     }
37     }
38     - mf << " $(OBJ)/LinkTimestamp.o -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)";
39     + mf << " $(OBJ)/LinkTimestamp.o $(PTHREAD_OBJ) -L. -L$(LIB) -L$(OBJ)";
40     + mf << " -l" << libname;
41     for ( set<string>::iterator dep_iter = lib_deps.begin();
42     dep_iter != lib_deps.end(); ++dep_iter )
43     mf << " " << "$(" << *dep_iter << "_LFLAGS)";
44     @@ -1208,7 +1209,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
45     sharedlib_name.erase( sharedlib_name.size() - 3, 3 );
46     mf << " -l" << sharedlib_name;
47     }
48     - mf << " -l" << libname;
49     + mf << " $(LINK_LIBS)";
50     mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n";
51     }
52     }
53     diff --git a/Makefile.in b/Makefile.in
54     index f20db27..fe45b4c 100644
55     --- a/Makefile.in
56     +++ b/Makefile.in
57     @@ -106,9 +106,9 @@ vpath % $(BIN)
58     ##############################################################################
59    
60     # our boost dependancies
61     -BOOST_FILESYSTEM_LFLAGS = -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
62     +BOOST_FILESYSTEM_LFLAGS = -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
63     BOOST_IOSTREAMS_LFLAGS = -lboost_iostreams-@BOOST_TAG@
64     -BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
65     +BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
66    
67     # PUT OUR GMP FLAGS HERE
68     GMP_LFLAGS = @GMP_LIB@
69     @@ -340,10 +340,10 @@ LINK_OPTIONS = \
70     $(PTHREAD_LINK)
71    
72     LINK_LIBS = \
73     + @LIBRARIES@ \
74     @LIBS@ \
75     $(OMP_LIBS) \
76     - $(PTHREAD_LIBS) \
77     - @LIBRARIES@
78     + $(PTHREAD_LIBS)
79    
80     CPPO = $(LINK_OPTIONS)
81     CPPC = $(CPP_OPTIONS) $(SYS_MEMTRACK)
82     @@ -420,10 +420,10 @@ execs_size:
83     MakeDepend: MakeDepend.cc
84     @ mkdir -p $(BIN)
85     echo $(PATH)
86     - $(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
87     + $(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) $(L_FLAGS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
88    
89     checkLock: $(SRC)/util/checkLock.cc
90     - $(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock
91     + $(CPLUSPLUS) $(CPPO) $(CPPC) $(SRC)/util/checkLock.cc $(L_FLAGS) -o $(BIN)/checkLock
92    
93     MemTracker.o: MemTracker.cc
94     @ mkdir -p $(OBJ)
95     diff --git a/Makefile_g++ b/Makefile_g++
96     index 8dc8572..2a29ecc 100644
97     --- a/Makefile_g++
98     +++ b/Makefile_g++
99     @@ -29,7 +29,8 @@ PIC = -fPIC
100     #############################################################
101    
102     # pThread library
103     -PTHREAD_LFLAGS = $(OBJ)/system/Threads.o -lpthread
104     +PTHREAD_LFLAGS = -lpthread
105     +PTHREAD_OBJ = $(OBJ)/system/Threads.o
106     PTHREAD_LIB = system/Threads.o
107    
108     #### Zlib library setup ####
109     diff --git a/TestProgram.cc b/TestProgram.cc
110     index e779fab..b480add 100644
111     --- a/TestProgram.cc
112     +++ b/TestProgram.cc
113     @@ -1,5 +1,6 @@
114     // MakeDepend: library BOOST_FILESYSTEM
115     // MakeDepend: library GMPXX
116     +// MakeDepend: library GMP
117     #include <gmpxx.h>
118     #include <iostream>
119     #include <boost/filesystem/path.hpp>
120     diff --git a/lookup/CreateLookupTab.cc b/lookup/CreateLookupTab.cc
121     index 44f2579..ac5c3bb 100644
122     --- a/lookup/CreateLookupTab.cc
123     +++ b/lookup/CreateLookupTab.cc
124     @@ -18,6 +18,9 @@
125     * This program just builds a singly-linked list of Locations for each kmer, and then walks each
126     * list to write them out to a feudal file.
127     */
128     +
129     +// MakeDepend: library BOOST_SYSTEM
130     +
131     #ifndef FORCE_DEBUG
132     #define NDEBUG
133     #endif
134     diff --git a/paths/AlignPairsToHyper3G.cc b/paths/AlignPairsToHyper3G.cc
135     index 5a0fda6..7b284a8 100644
136     --- a/paths/AlignPairsToHyper3G.cc
137     +++ b/paths/AlignPairsToHyper3G.cc
138     @@ -7,6 +7,8 @@
139     // can be responsible for its use, misuse, or functionality. //
140     /////////////////////////////////////////////////////////////////////////////
141    
142     +// MakeDepend: library BOOST_SYSTEM
143     +
144     #ifndef FORCE_DEBUG
145     #define NDEBUG
146     #endif
147     diff --git a/paths/ErrorCorrectJump.cc b/paths/ErrorCorrectJump.cc
148     index 40c8536..bb4d779 100644
149     --- a/paths/ErrorCorrectJump.cc
150     +++ b/paths/ErrorCorrectJump.cc
151     @@ -7,6 +7,8 @@
152     // can be responsible for its use, misuse, or functionality. //
153     /////////////////////////////////////////////////////////////////////////////
154    
155     +// MakeDepend: library BOOST_SYSTEM
156     +
157     #ifndef FORCE_DEBUG
158     #define NDEBUG
159     #endif
160     diff --git a/reporting/FastbStats.cc b/reporting/FastbStats.cc
161     index f87f295..ba7dbe3 100644
162     --- a/reporting/FastbStats.cc
163     +++ b/reporting/FastbStats.cc
164     @@ -8,6 +8,7 @@
165     /////////////////////////////////////////////////////////////////////////////
166    
167     // Basic stats for a fastb file.
168     +// MakeDepend: library BOOST_SYSTEM
169    
170     #include "Basevector.h"
171     #include "math/Functions.h"
172     diff --git a/util/FastaParser.cc b/util/FastaParser.cc
173     index 8b3dbc8..dc1d2cf 100644
174     --- a/util/FastaParser.cc
175     +++ b/util/FastaParser.cc
176     @@ -13,6 +13,9 @@
177     *
178     * \brief Several utility classes for reading FASTA files.
179     */
180     +
181     +// MakeDepend: library BOOST_SYSTEM
182     +
183     #ifndef FORCE_DEBUG
184     #define NDEBUG
185     #endif

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