sci-biology/ncbi-tools++: continuing with linking patches

Package-Manager: Portage-2.3.3, Repoman-2.3.1

8 files changed, 119 insertions, 0 deletions

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch
new file mode 100644
index 000000000..77b1ba05e
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch
@@ -0,0 +1,15 @@
+--- ncbi_cxx--18_0_0/src/app/hfilter/Makefile.hfilter.app.ori	2017-03-23 19:47:10.204018194 +0100
++++ ncbi_cxx--18_0_0/src/app/hfilter/Makefile.hfilter.app	2017-03-23 19:51:51.601108063 +0100
+@@ -5,9 +5,10 @@
+ APP = hfilter
+ SRC = hitfilter_app
+ 
+-LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS)
++LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \
++	xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ 
+-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+ 
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch
new file mode 100644
index 000000000..8610c7fd3
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch
@@ -0,0 +1,42 @@
+--- ncbi_cxx--18_0_0/src/app/igblast/Makefile.igblastn.app.ori	2017-03-23 20:30:35.667921836 +0100
++++ ncbi_cxx--18_0_0/src/app/igblast/Makefile.igblastn.app	2017-03-23 20:32:04.553561820 +0100
+@@ -2,7 +2,8 @@
+ 
+ APP = igblastn
+ SRC = igblastn_app
+-LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \
++	xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
+ 
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -10,7 +11,7 @@
+ CXXFLAGS = $(FAST_CXXFLAGS:ppc=i386)
+ LDFLAGS  = $(FAST_LDFLAGS:ppc=i386)
+ 
+-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/igblast/Makefile.igblastp.app.ori	2017-03-23 20:33:03.215124531 +0100
++++ ncbi_cxx--18_0_0/src/app/igblast/Makefile.igblastp.app	2017-03-23 20:34:22.817243181 +0100
+@@ -2,7 +2,8 @@
+ 
+ APP = igblastp
+ SRC = igblastp_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \
++	xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = blast_app_util igblast $(LIB_:%=%$(STATIC))
+ 
+ # De-universalize Mac builds to work around a PPC toolchain limitation
+@@ -10,7 +11,7 @@
+ CXXFLAGS = $(FAST_CXXFLAGS:ppc=i386)
+ LDFLAGS  = $(FAST_LDFLAGS:ppc=i386)
+ 
+-LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+ 
+ REQUIRES = objects -Cygwin
+ 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch
new file mode 100644
index 000000000..aacb20a6c
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app.ori	2017-03-23 21:12:52.028724998 +0100
++++ ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app	2017-03-23 21:13:30.079737366 +0100
+@@ -5,7 +5,7 @@
+ APP = ncfetch.cgi
+ SRC = ncfetch
+ 
+-LIB = xcgi xconnserv xconnect xutil xncbi
++LIB = xcgi xconnserv xthrserv xconnect xutil xncbi
+ LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+ 
+ WATCHERS = sadyrovr
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch
new file mode 100644
index 000000000..e074046cf
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori	2017-03-23 21:16:18.824226906 +0100
++++ ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app	2017-03-23 21:16:50.085058615 +0100
+@@ -4,7 +4,7 @@
+ SRC = netcache_cgi_sample
+ 
+ ### BEGIN COPIED SETTINGS
+-LIB = xconnserv xconnect xcgi xhtml xutil xncbi
++LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi
+ 
+ LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+ ### END COPIED SETTINGS
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch
new file mode 100644
index 000000000..f237a86d8
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app.ori	2017-03-23 21:22:14.463688886 +0100
++++ ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app	2017-03-23 21:22:48.854603873 +0100
+@@ -10,7 +10,7 @@
+ REQUIRES = MT Linux
+ 
+ 
+-LIB =  netstorage ncbi_xcache_netcache xconnserv \
++LIB =  netstorage ncbi_xcache_netcache xconnserv xthrserv \
+        $(SDBAPI_LIB) xconnect connssl xutil xncbi
+ LIBS = $(SDBAPI_LIBS) $(NETWORK_LIBS) $(GNUTLS_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+ 
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch
new file mode 100644
index 000000000..9435e8b6a
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app.ori	2017-03-23 21:41:31.084603405 +0100
++++ ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app	2017-03-23 21:45:47.601428174 +0100
+@@ -8,7 +8,7 @@
+ 
+ APP = speedtest
+ SRC = speedtest
+-LIB = prosplign xalgoalignutil xcleanup taxon3 valid valerr $(BLAST_LIBS) \
++LIB = prosplign xalgoalignutil taxon1 xalgoseq xcleanup taxon3 valid valerr $(BLAST_LIBS) \
+       xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC))
+ 
+ LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch
new file mode 100644
index 000000000..56f213f08
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app.ori	2017-03-23 22:08:16.937327984 +0100
++++ ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app	2017-03-23 22:09:19.208984755 +0100
+@@ -12,7 +12,7 @@
+ LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \
+       $(BLAST_DB_DATA_LOADER_LIBS) \
+       ncbi_xloader_lds2 lds2 sqlitewrapp \
+-      xqueryparse xalgoseq $(PCRE_LIB) \
++      xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \
+       $(BLAST_LIBS:%=%$(STATIC)) \
+       $(OBJMGR_LIBS:%=%$(STATIC))
+ 
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index ce5b4ddb8..3f3f4efc6 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -119,6 +119,13 @@ src_prepare() {
 		"${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
 		"${FILESDIR}"/${P}-fix-app-compartp-linking.patch
 		"${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
+		"${FILESDIR}"/${P}-fix-app-hfilter-linking.patch
+		"${FILESDIR}"/${P}-fix-app-igblast-linking.patch
+		"${FILESDIR}"/${P}-fix-ncfetch-linking.patch
+		"${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch
+		"${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch
+		"${FILESDIR}"/${P}-fix-speedtest-linking.patch
+		"${FILESDIR}"/${P}-fix-splign-linking.patch
 		)
 	#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
 	epatch ${PATCHES[@]}