/[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 1.2 - (show annotations) (download)
Wed Nov 20 07:29:19 2013 UTC (9 months, 1 week ago) by jlec
Branch: MAIN
CVS Tags: HEAD
Changes since 1.1: +0 -0 lines
FILE REMOVED
superseeded by sci-biology/allpathslg
Upstream wants anybody to move over

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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