From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1PpUYz-0003JU-4Q for garchives@archives.gentoo.org; Tue, 15 Feb 2011 23:44:09 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A64B0E0960; Tue, 15 Feb 2011 23:44:00 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 65711E0960 for ; Tue, 15 Feb 2011 23:44:00 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-CAMELLIA256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 49AC21B4163 for ; Tue, 15 Feb 2011 23:43:59 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id B381A8006A for ; Tue, 15 Feb 2011 23:43:58 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <0556e6d156adfe70616199e629fe3bbc20fceff7.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/staden/files/, sci-biology/staden/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/staden/files/rpath.patch sci-biology/staden/staden-2.0.0.ebuild sci-biology/staden/staden-2.0.0_beta8.ebuild X-VCS-Directories: sci-biology/staden/files/ sci-biology/staden/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 0556e6d156adfe70616199e629fe3bbc20fceff7 Date: Tue, 15 Feb 2011 23:43:58 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: b78c14edad78929f83cc80c7288c6072 commit: 0556e6d156adfe70616199e629fe3bbc20fceff7 Author: Martin Mokrejs gentoo org> AuthorDate: Tue Feb 15 23:43:34 2011 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Feb 15 23:43:34 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D0556e6d1 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 =3D> 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/fi= les/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_s= tubs/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 ---- + =20 + AC_SUBST(LD_LIBRARY_PATH_VAR) + =20 ++ AC_SUBST(CC_SEARCH_FLAGS) ++=20 + # 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 ---- + =20 + =20 + =20 ++=20 ++=20 + # These must be called after we do the basic CFLAGS checks and + # verify any possible 64-bit or similar switches are necessary + =20 +*************** +*** 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 + =20 +! if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` =3D= 53; then + break + elif $ac_last_try; then + { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&= 5 +--- 15909,15915 ---- + LTLIBOBJS!$LTLIBOBJS$ac_delim + _ACEOF + =20 +! if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed | grep -c X` =3D= 54; then + break + elif $ac_last_try; then + { { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&= 5 +diff -cr staden-2.0.0b8-src/staden.profile staden-2.0.0b8-src.orig/stade= n.profile +*** staden-2.0.0b8-src/staden.profile Wed Feb 9 11:40:00 2011 +--- staden-2.0.0b8-src.orig/staden.profile Tue Feb 15 15:12:37 2011 +*************** +*** 46,54 **** + then + [ x"$STADEN_PREPEND" !=3D "x" ] \ + && LD_LIBRARY_PATH=3D$STADLIB:$LD_LIBRARY_PATH \ +! || LD_LIBRARY_PATH=3D$LD_LIBRARY_PATH:$STADLIB + else +! LD_LIBRARY_PATH=3D$STADLIB + fi + export LD_LIBRARY_PATH + fi +--- 46,54 ---- + then + [ x"$STADEN_PREPEND" !=3D "x" ] \ + && LD_LIBRARY_PATH=3D$STADLIB:$LD_LIBRARY_PATH \ +! || LD_LIBRARY_PATH=3D$LD_LIBRARY_PATH:$STADLIB:$STADENROOT= /lib + else +! LD_LIBRARY_PATH=3D$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 =3D , + =20 ++ LIB_RUNTIME_DIR =3D ${prefix}/lib/staden + CC =3D @CC@ + #CDEBUG =3D -Wall -Wno-sign-compare -Wno-pointer-sign -Wno-parenthe= ses -Wno-unused -Wno-char-subscripts -Wno-pointer-to-int-cast -Wno-int-to= -pointer-cast + CFLAGS =3D @CFLAGS@ $(DEFINES) $(INCLUDES) +*************** +*** 68,76 **** + CXXFLAGS =3D @CXXFLAGS@ $(DEFINES) $(INCLUDES) + CPP =3D @CPP@ + CPPFLAGS =3D @CPPFLAGS@ +! LDFLAGS =3D -L$(L) @LDFLAGS@ + #CLDFLAGS =3D -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpa= th-link$(comma),$(filter -L%,$(IOLIB_LIB))) +! CLDFLAGS =3D -L$(L) + CXXLDFLAGS =3D $(CLDFLAGS) + F77 =3D @F77@ + FFLAGS =3D @FFLAGS@ +--- 69,77 ---- + CXXFLAGS =3D @CXXFLAGS@ $(DEFINES) $(INCLUDES) + CPP =3D @CPP@ + CPPFLAGS =3D @CPPFLAGS@ +! LDFLAGS =3D -L$(L) @LDFLAGS@ @CC_SEARCH_FLAGS@ + #CLDFLAGS =3D -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpa= th-link$(comma),$(filter -L%,$(IOLIB_LIB))) +! CLDFLAGS =3D -L$(L) @CC_SEARCH_FLAGS@ + CXXLDFLAGS =3D $(CLDFLAGS) + F77 =3D @F77@ + FFLAGS =3D @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: $ =20 @@ -6,9 +6,10 @@ EAPI=3D3 =20 inherit eutils flag-o-matic base =20 -DESCRIPTION=3D"A fully developed set of DNA sequence assembly (Gap4), ed= iting and analysis tools (Spin)." +DESCRIPTION=3D"DNA sequence assembly (gap4, gap5), editing and analysis = tools (Spin)." HOMEPAGE=3D"http://sourceforge.net/projects/staden" -SRC_URI=3D"http://downloads.sourceforge.net/staden/staden-2.0.0b7-src.ta= r.gz" +SRC_URI=3D"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" =20 LICENSE=3D"staden" SLOT=3D"0" @@ -38,11 +39,12 @@ RDEPEND=3D"tcl? ( >=3Ddev-tcltk/itcl-3.2 ) tk? ( >=3Ddev-tcltk/itk-3.2 ) >=3Ddev-tcltk/iwidgets-4.0" =20 -S=3D"${WORKDIR}"/staden-2.0.0b7-src +S=3D"${WORKDIR}"/staden-2.0.0b8-src =20 -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=3D/usr/= lib/staden patch" ./bootstrap || die "bootstrap failed" } =20 @@ -61,4 +63,6 @@ src_compile() { =20 src_install() { emake install DESTDIR=3D"${D}" || die "make install failed" + #cd "${WORKDIR}"/staden_doc-2.0.0b8-src || die "failed to cd "${WORKDIR= }"/staden_doc-2.0.0b8-src" + #make install prefix=3D"${D}"/usr || die "failed to install pre-created= docs from upstream" }