diff options
| -rw-r--r-- | sci-biology/staden/Manifest | 6 | ||||
| -rw-r--r-- | sci-biology/staden/files/rpath.patch | 123 | ||||
| -rw-r--r-- | sci-biology/staden/staden-2.0.0_beta8.ebuild (renamed from sci-biology/staden/staden-2.0.0.ebuild) | 18 |
3 files changed, 138 insertions, 9 deletions
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest index 9deab50c8..363b58ff5 100644 --- a/sci-biology/staden/Manifest +++ b/sci-biology/staden/Manifest @@ -1,4 +1,6 @@ -DIST staden-2.0.0b7-src.tar.gz 27414341 RMD160 453c0879e82fd6d445dff2ccb7747e0cd56158a4 SHA1 02fd09715acca0b31f4bb9f1a67ce4e204d9a20b SHA256 c8b293a72e63d6ccc05209ed0200e8bc3d75df6a6e44eb02aecb4713274a6034 -EBUILD staden-2.0.0.ebuild 1600 RMD160 124e220dacfaa58e265e3549e61be02a34cdcdb5 SHA1 0469fcbcbe07c48f46c7dbb275bfbf33cd62b90e SHA256 6defa2558e75a0a9f377439119b9ab3fd0d90c3ada3eb95eed8c7ec8d1136c81 +AUX rpath.patch 4178 RMD160 0d2c8778ff81bc122a9a8eb0b28e8a423172075d SHA1 1360f9cfaa02c15a8e7a9535ae1a02099501d1f5 SHA256 126be8f08307ebefb9312d4c1a63e8ee00ed4976440248fe1fe4d0ab7f2b4736 +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 +EBUILD staden-2.0.0_beta8.ebuild 1955 RMD160 790b5547af478377f33ea6d07c6bcf28ab179607 SHA1 c3fcf985db57e27908afd4919b199c5714dfd491 SHA256 4f4ebfeb56eda33988507fed93d882044838045326beb0f6f0e54a6da32b3715 EBUILD staden-9999.ebuild 2287 RMD160 dcdc6a912ea5eb074241f5483e9ac1f5160ef280 SHA1 db4440eb263d1b692e8187e021b4e0bad95b6b74 SHA256 258092dc0cfe3fd1f3a01e0c48b930d101f86936aab7853a9dda9cdec3a599bf MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/sci-biology/staden/files/rpath.patch b/sci-biology/staden/files/rpath.patch new file mode 100644 index 000000000..7bda2171e --- /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 index 3678c9293..a79bfd2fc 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" } |