/[gentoo-x86]/sci-biology/allpaths/files/allpaths-3.1-linking.patch
Gentoo

Contents of /sci-biology/allpaths/files/allpaths-3.1-linking.patch

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (show annotations) (download)
Wed Nov 20 07:29:19 2013 UTC (10 months 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 | 9 +++++----
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, 24 insertions(+), 9 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..289af1c 100644
55 --- a/Makefile.in
56 +++ b/Makefile.in
57 @@ -106,9 +106,10 @@ vpath % $(BIN)
58 ##############################################################################
59
60 # our boost dependancies
61 -BOOST_FILESYSTEM_LFLAGS = -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
62 +BOOST_SYSTEM = -lboost_system
63 +BOOST_FILESYSTEM_LFLAGS = -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
64 BOOST_IOSTREAMS_LFLAGS = -lboost_iostreams-@BOOST_TAG@
65 -BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
66 +BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
67
68 # PUT OUR GMP FLAGS HERE
69 GMP_LFLAGS = @GMP_LIB@
70 @@ -420,10 +421,10 @@ execs_size:
71 MakeDepend: MakeDepend.cc
72 @ mkdir -p $(BIN)
73 echo $(PATH)
74 - $(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
75 + $(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) $(L_FLAGS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
76
77 checkLock: $(SRC)/util/checkLock.cc
78 - $(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock
79 + $(CPLUSPLUS) $(CPPO) $(CPPC) $(SRC)/util/checkLock.cc $(L_FLAGS) -o $(BIN)/checkLock
80
81 MemTracker.o: MemTracker.cc
82 @ mkdir -p $(OBJ)
83 diff --git a/Makefile_g++ b/Makefile_g++
84 index 8dc8572..2a29ecc 100644
85 --- a/Makefile_g++
86 +++ b/Makefile_g++
87 @@ -29,7 +29,8 @@ PIC = -fPIC
88 #############################################################
89
90 # pThread library
91 -PTHREAD_LFLAGS = $(OBJ)/system/Threads.o -lpthread
92 +PTHREAD_LFLAGS = -lpthread
93 +PTHREAD_OBJ = $(OBJ)/system/Threads.o
94 PTHREAD_LIB = system/Threads.o
95
96 #### Zlib library setup ####
97 diff --git a/TestProgram.cc b/TestProgram.cc
98 index e779fab..b480add 100644
99 --- a/TestProgram.cc
100 +++ b/TestProgram.cc
101 @@ -1,5 +1,6 @@
102 // MakeDepend: library BOOST_FILESYSTEM
103 // MakeDepend: library GMPXX
104 +// MakeDepend: library GMP
105 #include <gmpxx.h>
106 #include <iostream>
107 #include <boost/filesystem/path.hpp>
108 diff --git a/lookup/CreateLookupTab.cc b/lookup/CreateLookupTab.cc
109 index 44f2579..ac5c3bb 100644
110 --- a/lookup/CreateLookupTab.cc
111 +++ b/lookup/CreateLookupTab.cc
112 @@ -18,6 +18,9 @@
113 * This program just builds a singly-linked list of Locations for each kmer, and then walks each
114 * list to write them out to a feudal file.
115 */
116 +
117 +// MakeDepend: library BOOST_SYSTEM
118 +
119 #ifndef FORCE_DEBUG
120 #define NDEBUG
121 #endif
122 diff --git a/paths/AlignPairsToHyper3G.cc b/paths/AlignPairsToHyper3G.cc
123 index 5a0fda6..7b284a8 100644
124 --- a/paths/AlignPairsToHyper3G.cc
125 +++ b/paths/AlignPairsToHyper3G.cc
126 @@ -7,6 +7,8 @@
127 // can be responsible for its use, misuse, or functionality. //
128 /////////////////////////////////////////////////////////////////////////////
129
130 +// MakeDepend: library BOOST_SYSTEM
131 +
132 #ifndef FORCE_DEBUG
133 #define NDEBUG
134 #endif
135 diff --git a/paths/ErrorCorrectJump.cc b/paths/ErrorCorrectJump.cc
136 index 40c8536..bb4d779 100644
137 --- a/paths/ErrorCorrectJump.cc
138 +++ b/paths/ErrorCorrectJump.cc
139 @@ -7,6 +7,8 @@
140 // can be responsible for its use, misuse, or functionality. //
141 /////////////////////////////////////////////////////////////////////////////
142
143 +// MakeDepend: library BOOST_SYSTEM
144 +
145 #ifndef FORCE_DEBUG
146 #define NDEBUG
147 #endif
148 diff --git a/reporting/FastbStats.cc b/reporting/FastbStats.cc
149 index f87f295..ba7dbe3 100644
150 --- a/reporting/FastbStats.cc
151 +++ b/reporting/FastbStats.cc
152 @@ -8,6 +8,7 @@
153 /////////////////////////////////////////////////////////////////////////////
154
155 // Basic stats for a fastb file.
156 +// MakeDepend: library BOOST_SYSTEM
157
158 #include "Basevector.h"
159 #include "math/Functions.h"
160 diff --git a/util/FastaParser.cc b/util/FastaParser.cc
161 index 8b3dbc8..dc1d2cf 100644
162 --- a/util/FastaParser.cc
163 +++ b/util/FastaParser.cc
164 @@ -13,6 +13,9 @@
165 *
166 * \brief Several utility classes for reading FASTA files.
167 */
168 +
169 +// MakeDepend: library BOOST_SYSTEM
170 +
171 #ifndef FORCE_DEBUG
172 #define NDEBUG
173 #endif

  ViewVC Help
Powered by ViewVC 1.1.20