[gentoo-commits] proj/sci:master commit in: sci-biology/staden/files/, sci-biology/staden/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     0556e6d156adfe70616199e629fe3bbc20fceff7
Author:     Martin Mokrejs <mmokrejs <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 15 23:43:34 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 15 23:43:34 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0556e6d1

sci-biology/staden-2.0.0_beta8: new release

(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/staden/files/rpath.patch               |  123 ++++++++++++++++++++
 ...aden-2.0.0.ebuild => staden-2.0.0_beta8.ebuild} |   18 ++-
 2 files changed, 134 insertions(+), 7 deletions(-)

diff --git a/sci-biology/staden/files/rpath.patch b/sci-biology/staden/files/rpath.patch
new file mode 100644
index 0000000..7bda217
--- /dev/null
+++ b/sci-biology/staden/files/rpath.patch
@@ -0,0 +1,123 @@
+diff -cr staden-2.0.0b8-src/ac_stubs/tcl.m4 staden-2.0.0b8-src.orig/ac_stubs/tcl.m4
+*** staden-2.0.0b8-src/ac_stubs/tcl.m4	Wed Feb  9 11:40:00 2011
+--- staden-2.0.0b8-src.orig/ac_stubs/tcl.m4	Tue Feb 15 15:12:37 2011
+***************
+*** 2245,2250 ****
+--- 2245,2252 ----
+  
+      AC_SUBST(LD_LIBRARY_PATH_VAR)
+  
++     AC_SUBST(CC_SEARCH_FLAGS)
++ 
+      # These must be called after we do the basic CFLAGS checks and
+      # verify any possible 64-bit or similar switches are necessary
+      TEA_TCL_EARLY_FLAGS
+diff -cr staden-2.0.0b8-src/configure staden-2.0.0b8-src.orig/configure
+*** staden-2.0.0b8-src/configure	Wed Feb  9 11:39:59 2011
+--- staden-2.0.0b8-src.orig/configure	Tue Feb 15 15:12:37 2011
+***************
+*** 745,750 ****
+--- 745,751 ----
+  SHLIB_LD_LIBS
+  SHLIB_CFLAGS
+  LD_LIBRARY_PATH_VAR
++ CC_SEARCH_FLAGS
+  TCL_INCLUDES
+  TCL_TOP_DIR_NATIVE
+  TK_INCLUDES
+***************
+*** 13888,13893 ****
+--- 13889,13896 ----
+  
+  
+  
++ 
++ 
+      # These must be called after we do the basic CFLAGS checks and
+      # verify any possible 64-bit or similar switches are necessary
+  
+***************
+*** 15886,15891 ****
+--- 15889,15895 ----
+  SHLIB_LD_LIBS!$SHLIB_LD_LIBS$ac_delim
+  SHLIB_CFLAGS!$SHLIB_CFLAGS$ac_delim
+  LD_LIBRARY_PATH_VAR!$LD_LIBRARY_PATH_VAR$ac_delim
++ CC_SEARCH_FLAGS!$CC_SEARCH_FLAGS$ac_delim
+  TCL_INCLUDES!$TCL_INCLUDES$ac_delim
+  TCL_TOP_DIR_NATIVE!$TCL_TOP_DIR_NATIVE$ac_delim
+  TK_INCLUDES!$TK_INCLUDES$ac_delim
+***************
+*** 15905,15911 ****
+  LTLIBOBJS!$LTLIBOBJS$ac_delim
+  _ACEOF
+  
+!   if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 53; then
+      break
+    elif $ac_last_try; then
+      { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+--- 15909,15915 ----
+  LTLIBOBJS!$LTLIBOBJS$ac_delim
+  _ACEOF
+  
+!   if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` = 54; then
+      break
+    elif $ac_last_try; then
+      { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+diff -cr staden-2.0.0b8-src/staden.profile staden-2.0.0b8-src.orig/staden.profile
+*** staden-2.0.0b8-src/staden.profile	Wed Feb  9 11:40:00 2011
+--- staden-2.0.0b8-src.orig/staden.profile	Tue Feb 15 15:12:37 2011
+***************
+*** 46,54 ****
+          then
+              [ x"$STADEN_PREPEND" != "x" ] \
+              && LD_LIBRARY_PATH=$STADLIB:$LD_LIBRARY_PATH \
+!             || LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$STADLIB
+          else
+!             LD_LIBRARY_PATH=$STADLIB
+          fi
+          export LD_LIBRARY_PATH
+      fi
+--- 46,54 ----
+          then
+              [ x"$STADEN_PREPEND" != "x" ] \
+              && LD_LIBRARY_PATH=$STADLIB:$LD_LIBRARY_PATH \
+!             || LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$STADLIB:$STADENROOT/lib
+          else
+!             LD_LIBRARY_PATH=$STADLIB:$STADENROOT/lib
+          fi
+          export LD_LIBRARY_PATH
+      fi
+diff -cr staden-2.0.0b8-src/system.mk.in staden-2.0.0b8-src.orig/system.mk.in
+*** staden-2.0.0b8-src/system.mk.in	Wed Feb  9 11:40:00 2011
+--- staden-2.0.0b8-src.orig/system.mk.in	Tue Feb 15 15:12:37 2011
+***************
+*** 61,66 ****
+--- 61,67 ----
+  # How else do we get commas in a subst text or pattern?
+  comma = ,
+  
++ LIB_RUNTIME_DIR   = ${prefix}/lib/staden
+  CC		  = @CC@
+  #CDEBUG		  = -Wall -Wno-sign-compare -Wno-pointer-sign -Wno-parentheses -Wno-unused -Wno-char-subscripts -Wno-pointer-to-int-cast -Wno-int-to-pointer-cast
+  CFLAGS		  = @CFLAGS@ $(DEFINES) $(INCLUDES)
+***************
+*** 68,76 ****
+  CXXFLAGS	  = @CXXFLAGS@ $(DEFINES) $(INCLUDES)
+  CPP		  = @CPP@
+  CPPFLAGS	  = @CPPFLAGS@
+! LDFLAGS		  = -L$(L) @LDFLAGS@
+  #CLDFLAGS	  = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
+! CLDFLAGS	  = -L$(L)
+  CXXLDFLAGS	  = $(CLDFLAGS)
+  F77		  = @F77@
+  FFLAGS		  = @FFLAGS@
+--- 69,77 ----
+  CXXFLAGS	  = @CXXFLAGS@ $(DEFINES) $(INCLUDES)
+  CPP		  = @CPP@
+  CPPFLAGS	  = @CPPFLAGS@
+! LDFLAGS		  = -L$(L) @LDFLAGS@ @CC_SEARCH_FLAGS@
+  #CLDFLAGS	  = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
+! CLDFLAGS	  = -L$(L) @CC_SEARCH_FLAGS@
+  CXXLDFLAGS	  = $(CLDFLAGS)
+  F77		  = @F77@
+  FFLAGS		  = @FFLAGS@

diff --git a/sci-biology/staden/staden-2.0.0.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild
similarity index 64%
rename from sci-biology/staden/staden-2.0.0.ebuild
rename to sci-biology/staden/staden-2.0.0_beta8.ebuild
index 3678c92..a79bfd2 100644
--- a/sci-biology/staden/staden-2.0.0.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -6,9 +6,10 @@ EAPI=3
 
 inherit eutils flag-o-matic base
 
-DESCRIPTION="A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin)."
+DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)."
 HOMEPAGE="http://sourceforge.net/projects/staden"
-SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b7-src.tar.gz"
+SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz
+		http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz"
 
 LICENSE="staden"
 SLOT="0"
@@ -38,11 +39,12 @@ RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 )
 		tk? ( >=dev-tcltk/itk-3.2 )
 		>=dev-tcltk/iwidgets-4.0"
 
-S="${WORKDIR}"/staden-2.0.0b7-src
+S="${WORKDIR}"/staden-2.0.0b8-src
 
-src_unpack() {
-	unpack ${A}
-	cd "${S}" || die "Cannot cd ${WORKDIR}/staden-2.0.0b7-src"
+src_prepare() {
+	unpack ${A} || die
+	cd "${S}" || die "Cannot cd ${WORKDIR}/staden-2.0.0b8-src"
+	epatch "${FILESDIR}"/rpath.patch || die "failed to apply -rpath=/usr/lib/staden patch"
 	./bootstrap || die "bootstrap failed"
 }
 
@@ -61,4 +63,6 @@ src_compile() {
 
 src_install() {
 	emake install DESTDIR="${D}" || die "make install failed"
+	#cd "${WORKDIR}"/staden_doc-2.0.0b8-src || die "failed to cd "${WORKDIR}"/staden_doc-2.0.0b8-src"
+	#make install prefix="${D}"/usr || die "failed to install pre-created docs from upstream"
 }