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

[Martin Mokrejs]

commit:     f88f1a0e9b529e9ca95ecec39f080675a4ae20de
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 25 23:24:16 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jun 25 23:24:16 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f88f1a0e

sci-biology/ncbi-tools++-12.0.0: dropped unneeded patches, added direct dependency on glew because the dependency on virtual/opengl does not work

---
 .../files/ncbi-tools++-12.0.0-linking.patch        | 52 ----------------------
 .../files/ncbi-tools++-12.0.0-linking2.patch       | 10 -----
 .../ncbi-tools++/ncbi-tools++-12.0.0.ebuild        |  7 +--
 3 files changed, 2 insertions(+), 67 deletions(-)

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
deleted file mode 100644
index 196f3a4..0000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking.patch
+++ /dev/null
@@ -1,52 +0,0 @@
---- ncbi_cxx--12_0_0/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib.ori   (revision 400707)
-+++ ncbi_cxx--12_0_0/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib   (working copy)
-@@ -10,6 +10,6 @@
- LIB_OR_DLL = both
- 
- # Dependencies for shared library
--DLL_LIB = ncbi_xreader$(DLL)
-+DLL_LIB = $(GENBANK_LDEP)
- 
- WATCHERS = vasilche
---- ncbi_cxx--12_0_0/src/app/grid/util/Makefile.ncfetch.app.ori  (revision 400707)
-+++ ncbi_cxx--12_0_0/src/app/grid/util/Makefile.ncfetch.app  (working copy)
-@@ -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 = kazimird
---- ncbi_cxx--12_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori    (revision 400707)
-+++ ncbi_cxx--12_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app    (working copy)
-@@ -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) $(ORIG_LIBS)
- ### END COPIED SETTINGS
---- ncbi_cxx--12_0_0/src/misc/grid_cgi/Makefile.xgridcgi.lib.ori        2014-06-24 21:42:11.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/misc/grid_cgi/Makefile.xgridcgi.lib    2014-06-24 21:42:29.000000000 +0200
-@@ -10,4 +10,4 @@
-
- WATCHERS = vakatov
-
--DLL_LIB = xncbi xcgi xconnserv xhtml
-+DLL_LIB = xhtml xcgi xconnserv
---- ncbi_cxx--12_0_0/src/sra/sdk/libs/vfs/Makefile.vfs.lib.ori	2014-06-24 22:54:55.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/sra/sdk/libs/vfs/Makefile.vfs.lib	2014-06-24 22:55:05.000000000 +0200
-@@ -8,6 +8,7 @@
- CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \
-            $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE $(ORIG_CPPFLAGS)
- 
--DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL)
-+DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) krypto$(DLL) \
-+          kfg$(DLL) kfs$(DLL) klib$(DLL)
- 
- LIB_OR_DLL = both
-

diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
deleted file mode 100644
index 5507b84..0000000
--- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linking2.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- ncbi_cxx--12_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori	2014-06-24 21:50:43.000000000 +0200
-+++ ncbi_cxx--12_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app	2014-06-24 21:50:48.000000000 +0200
-@@ -11,7 +11,7 @@
- # the lines reading "### BEGIN/END COPIED SETTINGS" in any way.
- 
- ### BEGIN COPIED SETTINGS
--LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi
-+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi
- 
- LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 746a3fe..d8b7d97 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -42,7 +42,7 @@ DEPEND="
 	mysql? ( virtual/mysql )
 	ssl? ( dev-libs/openssl )
 	fltk? ( x11-libs/fltk )
-	opengl? ( virtual/opengl )
+	opengl? ( virtual/opengl media-libs/glew )
 	mesa? ( media-libs/mesa
 		media-libs/glew
 	)
@@ -72,7 +72,7 @@ DEPEND="
 # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
 
 
-# seems muParser is required, also glew is required. configure exits otherwise
+# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled)
 
 RDEPEND="${DEPEND}"
 
@@ -117,9 +117,6 @@ src_prepare() {
 #       "${FILESDIR}"/${P}-as-needed.patch
 #       "${FILESDIR}"/${P}-fix-creaders-linking.patch
 #       "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
-# replaced by -linkage-tuneups.patch
-#		"${FILESDIR}"/${P}-linking.patch
-#		"${FILESDIR}"/${P}-linking2.patch
 #		)
 		# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
 	epatch ${PATCHES[@]}