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path: root/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch
blob: 43104976e10c58394e5346427805067d55e6fc3d (plain) 
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--- ncbi_cxx--18_0_0/src/app/blast/Makefile.blast_formatter.app.ori	2017-03-22 17:21:05.653409646 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.blast_formatter.app	2017-03-22 17:22:25.755581547 +0100
@@ -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
@@ -11,6 +11,6 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.blastn.app.ori	2017-03-22 19:57:18.063352028 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.blastn.app	2017-03-22 19:58:28.925273217 +0100
@@ -14,7 +14,7 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
 
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.blastp.app.ori	2017-03-22 19:57:18.063352028 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.blastp.app	2017-03-22 19:58:54.365962959 +0100
@@ -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
@@ -13,7 +13,7 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
 
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.blastx.app.ori	2017-03-22 19:57:18.063352028 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.blastx.app	2017-03-22 19:59:11.066415737 +0100
@@ -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
@@ -13,7 +13,7 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
 
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.deltablast.app.ori	2017-03-22 19:57:18.063352028 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.deltablast.app	2017-03-22 19:59:30.396939821 +0100
@@ -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
@@ -10,6 +10,6 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.psiblast.app.ori	2017-03-22 19:57:18.063352028 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.psiblast.app	2017-03-22 19:59:51.837521114 +0100
@@ -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
@@ -11,6 +11,6 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.rpsblast.app.ori	2017-03-22 19:57:18.063352028 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.rpsblast.app	2017-03-22 20:00:15.808170999 +0100
@@ -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
@@ -11,6 +11,6 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.rpstblastn.app.ori	2017-03-22 19:57:18.063352028 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.rpstblastn.app	2017-03-22 20:00:34.328673121 +0100
@@ -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
@@ -11,6 +11,6 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.seedtop.app.ori	2017-03-22 19:57:18.073352297 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.seedtop.app	2017-03-22 20:00:52.309160604 +0100
@@ -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
@@ -11,6 +11,6 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.tblastn.app.ori	2017-03-22 19:57:18.073352297 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.tblastn.app	2017-03-22 20:01:09.669631276 +0100
@@ -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
@@ -13,7 +13,7 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin
 
--- ncbi_cxx--18_0_0/src/app/blast/Makefile.tblastx.app.ori	2017-03-22 19:57:18.073352297 +0100
+++ ncbi_cxx--18_0_0/src/app/blast/Makefile.tblastx.app	2017-03-22 20:01:23.860016002 +0100
@@ -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
@@ -13,7 +13,7 @@
 LDFLAGS  = $(FAST_LDFLAGS:ppc=i386) 
 
 CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
+LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
 
 REQUIRES = objects -Cygwin