sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch


1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130

Index: c++.18.0.0/src/app/blast/Makefile.blast_formatter.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.blast_formatter.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.blast_formatter.app	(working copy)
@@ -2,7 +2,7 @@
 
 APP = blast_formatter
 SRC = blast_formatter
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation
Index: c++.18.0.0/src/app/blast/Makefile.blastp.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.blastp.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.blastp.app	(working copy)
@@ -4,7 +4,7 @@
 
 APP = blastp
 SRC = blastp_app
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation
Index: c++.18.0.0/src/app/blast/Makefile.blastx.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.blastx.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.blastx.app	(working copy)
@@ -4,7 +4,7 @@
 
 APP = blastx
 SRC = blastx_app
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation
Index: c++.18.0.0/src/app/blast/Makefile.deltablast.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.deltablast.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.deltablast.app	(working copy)
@@ -1,7 +1,7 @@
 
 APP = deltablast
 SRC = deltablast_app
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation
Index: c++.18.0.0/src/app/blast/Makefile.psiblast.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.psiblast.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.psiblast.app	(working copy)
@@ -2,7 +2,7 @@
 
 APP = psiblast
 SRC = psiblast_app
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation
Index: c++.18.0.0/src/app/blast/Makefile.rpsblast.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.rpsblast.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.rpsblast.app	(working copy)
@@ -2,7 +2,7 @@
 
 APP = rpsblast
 SRC = rpsblast_app
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation
Index: c++.18.0.0/src/app/blast/Makefile.rpstblastn.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.rpstblastn.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.rpstblastn.app	(working copy)
@@ -2,7 +2,7 @@
 
 APP = rpstblastn
 SRC = rpstblastn_app
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation
Index: c++.18.0.0/src/app/blast/Makefile.seedtop.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.seedtop.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.seedtop.app	(working copy)
@@ -2,7 +2,7 @@
 
 APP = seedtop
 SRC = seedtop_app
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation
Index: c++.18.0.0/src/app/blast/Makefile.tblastn.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.tblastn.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.tblastn.app	(working copy)
@@ -4,7 +4,7 @@
 
 APP = tblastn
 SRC = tblastn_app
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation
Index: c++.18.0.0/src/app/blast/Makefile.tblastx.app
===================================================================
--- c++.18.0.0/src/app/blast/Makefile.tblastx.app	(revision 523253)
+++ c++.18.0.0/src/app/blast/Makefile.tblastx.app	(working copy)
@@ -4,7 +4,7 @@
 
 APP = tblastx
 SRC = tblastx_app
-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
 LIB = blast_app_util $(LIB_:%=%$(STATIC))
 
 # De-universalize Mac builds to work around a PPC toolchain limitation