sci-biology/staden: Version Bump, move to sane portage like building

Package-Manager: portage-2.2.0_alpha142

7 files changed, 106 insertions, 148 deletions

diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index e98e9ca7d..0a9092b5d 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -1,7 +1,15 @@
 # ChangeLog for sci-biology/staden
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*staden-2.0.0_beta9 (26 Nov 2012)
+
+  26 Nov 2012; Justin Lecher <jlec@gentoo.org> -staden-2.0.0_beta8.ebuild,
+  +staden-2.0.0_beta9.ebuild, +files/staden-2.0.0_beta9-ldflags.patch,
+  +files/staden-2.0.0_beta9-libpng-1.5.patch,
+  +files/staden-2.0.0_beta9-zlib.patch, -files/rpath.patch:
+  Version Bump, move to sane portage like building
+
   12 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> staden-9999.ebuild:
   fix determination of svn-based checkout number required for building
   staden-9999.ebuild
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
index f75525948..8198edd23 100644
--- a/sci-biology/staden/Manifest
+++ b/sci-biology/staden/Manifest
@@ -1,2 +1,2 @@
-DIST staden-2.0.0b8.tar.gz 4312143 RMD160 68b91a80fae29e0bf8f7e6ca1c0781591113684c SHA1 742092ff7bfb5acd3376ac85d5ab50507d1dd02f SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d
-DIST staden_doc-2.0.0b8-src.tar.gz 3068758 RMD160 4844c3b5acc1ef16c438f66313e1a8b3c182edc2 SHA1 daa6f0702fa250817fbdd07f932cdf0ed993c6c2 SHA256 77dbf83ef674affb5ee21b6ac7875e8c36446092e076e4d99cffbc4b2220c65f
+DIST staden-2.0.0b9-src.tar.gz 4431301 SHA256 2cad8cc9821c83539e683f2bb28bbbfccbefb5bff589f71501b5cf53de8f4a8b SHA512 0818b376b9921c07cfdd36b6a62b615a3396153bbcb8714a852148457a5cc190da32af318777f07da7012e5cb45d352e8b13884176e1e85fd1707f36adff972e WHIRLPOOL 16e4070dfea1e1de30c1d7bf0e2a6c1be27c4a5364ab4e82b4bd7aea0bd4e97cfdf4e020dd418860cb79d1906bd830de94023edf1a1dc8715bdcabfb9a03141a
+DIST staden_doc-2.0.0b9-src.tar.gz 3181687 SHA256 942a560e22de0fd0da8856d2049fba1703ea042e7ea5b80e277a2d57d7fe4cd4 SHA512 9f1d1ec7f8301058574ec7da604274d1767258293c88f6cde6426ad361a8543833fa4b755e5f0109ca4dd88ea41cd7fa94f2f7e14a4d9a516ec06ae49540c15f WHIRLPOOL f5adfdd6868d565c2269b13a45ae7d19a369f61679ac918aa8e02c64667e3117fb5a4efc717d06a8bf538c75a29a24580663308ca87d4192d837c9298a5808d2
diff --git a/sci-biology/staden/files/rpath.patch b/sci-biology/staden/files/rpath.patch
deleted file mode 100644
index 7bda2171e..000000000
--- a/sci-biology/staden/files/rpath.patch
+++ /dev/null
@@ -1,123 +0,0 @@
-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/files/staden-2.0.0_beta9-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch
new file mode 100644
index 000000000..735feb315
--- /dev/null
+++ b/sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch
@@ -0,0 +1,30 @@
+ abi/Makefile | 2 +-
+ alf/Makefile | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/abi/Makefile b/abi/Makefile
+index 3c1f8fb..58b4353 100644
+--- a/abi/Makefile
++++ b/abi/Makefile
+@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
+ 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
+ 
+ getABIdate: $(OBJSD)
+-	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
++	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
+ 
+ getABIcomment: $(OBJSC)
+ 	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
+diff --git a/alf/Makefile b/alf/Makefile
+index 94b7480..ef41a26 100644
+--- a/alf/Makefile
++++ b/alf/Makefile
+@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
+ ALFOBJ = alfsplit.o
+ 
+ alfsplit: $(ALFOBJ)
+-	$(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
++	$(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
+ 
+ RSOBJ = $(ALFBIN)/2rs.o
+ 
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch b/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch
new file mode 100644
index 000000000..50694a8eb
--- /dev/null
+++ b/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch
@@ -0,0 +1,16 @@
+ tk_utils/tkTrace.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tk_utils/tkTrace.c b/tk_utils/tkTrace.c
+index beeb478..42a4e11 100644
+--- a/tk_utils/tkTrace.c
++++ b/tk_utils/tkTrace.c
+@@ -2123,7 +2123,7 @@ int drawable_to_png(DNATrace *t, FILE *fp, Display *disp, Drawable d,
+ 	goto error;
+ 
+     /* PNG requires setjmp/longjmp to be used */
+-    if (setjmp(png_ptr->jmpbuf))
++    if (setjmp (png_jmpbuf (png_ptr)))
+ 	goto error;
+ 
+     /* Create the info bits */
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch b/sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch
new file mode 100644
index 000000000..39537604e
--- /dev/null
+++ b/sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch
@@ -0,0 +1,16 @@
+ gap5/zfio.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/gap5/zfio.c b/gap5/zfio.c
+index 35da12a..1b628e4 100644
+--- a/gap5/zfio.c
++++ b/gap5/zfio.c
+@@ -51,7 +51,7 @@ int zfpeek(zfp *zf) {
+ 	if (c != EOF)
+ 	    ungetc(c, zf->fp);
+     } else {
+-	c = gzgetc(zf->gz);
++	c = gzgetc((gzFile)zf->gz);
+ 	if (c != EOF)
+ 	    gzungetc(c, zf->gz);
+     }
diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta9.ebuild
index 88a6147a7..b1d51c1d2 100644
--- a/sci-biology/staden/staden-2.0.0_beta8.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta9.ebuild
@@ -1,16 +1,18 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
 
-inherit base eutils flag-o-matic fortran-2 multilib
+AUTOTOOLS_AUTORECONF=yes
+
+inherit autotools-utils eutils flag-o-matic fortran-2 multilib
 
 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-2.0.0b8.tar.gz
-	http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz"
+	http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz
+	http://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
 
 LICENSE="staden"
 SLOT="0"
@@ -28,38 +30,47 @@ DEPEND="
 	app-arch/xz-utils
 	dev-lang/tk
 	dev-tcltk/tklib
-	>=media-libs/libpng-1.2
+	media-libs/libpng:0
 	sci-biology/samtools
 	>=sci-libs/io_lib-1.12.2
-	>=sys-libs/zlib-1.2
-	virtual/fortran"
+	sys-libs/zlib"
 RDEPEND="${DEPEND}
 	>=dev-tcltk/iwidgets-4.0
 	tcl? ( >=dev-tcltk/itcl-3.2 )
 	tk? ( >=dev-tcltk/itk-3.2 )"
 
-S="${WORKDIR}"/staden-2.0.0b8-src
+S="${WORKDIR}"/staden-${PV/_beta/b}-src
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+PATCHES=(
+	"${FILESDIR}"/${P}-ldflags.patch
+	"${FILESDIR}"/${P}-libpng-1.5.patch
+	"${FILESDIR}"/${P}-zlib.patch )
 
 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"
+	sed \
+		-e 's:svnversion:false:' \
+		-i configure.in || die
+
+	AT_M4DIR=ac_stubs autotools-utils_src_prepare
 }
 
 src_configure(){
-	local myconf
-	use X && myconf=" --with-x"
-	myconf=" --with-tklib=/usr/lib/tklib0.5" # HACK
-	use amd64 && myconf="${myconf} --enable-64bit"
+	local myeconfargs=()
+	use X && myeconfargs+=( --with-x )
+	myeconfargs+=(
+		--with-tklib=/usr/$(get_libdir)/tklib
+		)
+	use amd64 && myeconfargs+=( --enable-64bit )
 	use debug && append-cflags "-DCACHE_REF_DEBUG"
-	econf ${myconf}
+	autotools-utils_src_configure
 }
 
 src_install() {
+	autotools-utils_src_install
 	# TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
-	emake install DESTDIR="${D}" || die "make install failed"
-	#cd "${WORKDIR}"/staden_doc-2.0.0b8-src || die "failed to cd "${WORKDIR}"/staden_doc-2.0.0b8-src"
+	#cd "${WORKDIR}"/staden_doc-${PV/_beta/b}-src || die "failed to cd "${WORKDIR}"/staden_doc-${PV/_beta/b}-src"
 	#make install prefix="${D}"/usr || die "failed to install pre-created docs from upstream"
 
 	# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
@@ -67,7 +78,7 @@ src_install() {
 	# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
 	# somehow for gap2caf, for example
 	cat >> "${T}"/99staden <<- EOF
-	LDPATH=/usr/$(get_libdir)/staden
+	LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
 	EOF
-	doenvd 99staden
+	doenvd "${T}"/99staden
 }