commit: 74d160e9dc55ef771da05ac064bfbe3f2ccd2cfb
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 26 20:37:15 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 26 20:37:15 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=74d160e9
sci-biology/ncbi-tools++: more fixes
Package-Manager: Portage-2.3.3, Repoman-2.3.1
.../files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch | 11 +++++++++++
.../files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch | 7 +++++--
.../files/ncbi-tools++-18.0.0-remove-old-symlinks.patch | 10 ++++++++++
sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 2 ++
4 files changed, 28 insertions(+), 2 deletions(-)
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
new file mode 100644
index 000000000..fce7263b2
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app.ori
2017-03-26 18:49:50.431994978 +0200
++++ ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app 2017-03-26
18:50:11.222552131 +0200
+@@ -2,7 +2,7 @@
+
+ APP = rmblastn
+ SRC = rmblastn_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
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
index 0724fa2cf..2568662f5 100644
---
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch
@@ -7,7 +7,10 @@
-LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \
- gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS)
+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \
-+ xobjutil entrez2cli entrez2 tables $(OBJMGR_LIBS)
++ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS)
- LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+-LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)
++LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS)
+
+ REQUIRES = objects -Cygwin
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch
new file mode 100644
index 000000000..098a9ad1e
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch
@@ -0,0 +1,10 @@
+--- ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in.old
2017-03-26 19:01:58.101495278 +0200
++++ ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in
2017-03-26 19:02:16.581990522 +0200
+@@ -13,6 +13,7 @@
+ -a ! -d $(libdir)/64 ]; then \
+ cd $(libdir) && $(LN_S) . 64; \
+ fi
++ $(RM) $(LINK)
+ cd $(libdir) && $(LN_S) libpython_ncbi_dbapi$(loadable_ext) $(LINK)
+
+ clean:;
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index f3bf993b0..02426ab42 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -127,6 +127,8 @@ src_prepare() {
"${FILESDIR}"/${P}-fix-speedtest-linking.patch
"${FILESDIR}"/${P}-fix-splign-linking.patch
"${FILESDIR}"/${P}-fix-srcchk-linking.patch
+ "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
+ "${FILESDIR}"/${P}-remove-old-symlinks.patch
)
#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
epatch ${PATCHES[@]}
