[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/

[Martin Mokrejs]

commit:     339162f1f266f025acebcffc1225961c3a50a24b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 27 00:44:01 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 27 00:44:01 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=339162f1

sci-biology/ncbi-tools++: and more

Package-Manager: Portage-2.3.5, Repoman-2.3.1

 .../ncbi-tools++-18.0.0-fix-app-tls-linking.patch     | 11 +++++++++++
 ...cbi-tools++-18.0.0-fix-app-vecscreen-linking.patch | 19 +++++++++++++++++++
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild   |  2 ++
 3 files changed, 32 insertions(+)

diff --git 
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch 
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch
new file mode 100644
index 000000000..541dc2514
--- /dev/null
+++ 
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app.ori  2017-03-27 
02:33:36.312151540 +0200
++++ ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app      2017-03-27 
02:34:19.372151184 +0200
+@@ -10,7 +10,7 @@
+ SRC = tls
+ 
+ LIB = $(OBJEDIT_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil \
+-       xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
++       xregexp $(PCRE_LIB) tables $(OBJMGR_LIBS)
+ 
+ LIBS = $(PCRE_LIBS) \
+        $(NETWORK_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS)

diff --git 
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
 
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
new file mode 100644
index 000000000..9f33392d3
--- /dev/null
+++ 
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch
@@ -0,0 +1,19 @@
+--- ncbi_cxx--18_0_0/src/app/vecscreen/Makefile.vecscreen.app.ori      
2017-03-27 02:34:44.242150979 +0200
++++ ncbi_cxx--18_0_0/src/app/vecscreen/Makefile.vecscreen.app  2017-03-27 
02:36:22.752150165 +0200
+@@ -4,7 +4,7 @@
+ 
+ APP = vecscreen
+ SRC = vecscreen_app
+-LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS)
++LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
+ LIB = $(LIB_:%=%$(STATIC))
+ # FIXME: do we need blast_app_util
+ #LIB = blast_app_util $(LIB_:%=%$(STATIC))
+@@ -15,6 +15,6 @@
+ LDFLAGS  = $(FAST_LDFLAGS:ppc=i386)
+ 
+ CPPFLAGS = $(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

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 40db6cfa3..5d0547875 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -130,6 +130,8 @@ src_prepare() {
                "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
                "${FILESDIR}"/${P}-remove-old-symlinks.patch
                "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
+               "${FILESDIR}"/${P}-fix-app-tls-linking.patch
+               "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
                )
        #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
        epatch ${PATCHES[@]}