poa: merged to gentoo-x86

13 files changed, 0 insertions, 241 deletions

diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
deleted file mode 100644
index f1a35e5..0000000
--- a/sci-biology/poa/Manifest
+++ /dev/null
@@ -1,32 +0,0 @@
-AUX add-libint-error-message.patch 722 RMD160 526e57d715b65fedc763069be30f7e49e52dcbb8 SHA1 862de3880c5ccebb4689440eaf7eaae9921cf0b7 SHA256 63715cab509893817c7cfb22422c3724fd02a4d0fa5065bbb5a477d8d8a23390
-MD5 74eaf8b13786493ed6220c0c33e09b28 files/add-libint-error-message.patch 722
-RMD160 526e57d715b65fedc763069be30f7e49e52dcbb8 files/add-libint-error-message.patch 722
-SHA256 63715cab509893817c7cfb22422c3724fd02a4d0fa5065bbb5a477d8d8a23390 files/add-libint-error-message.patch 722
-AUX dont-build-libint.patch 355 RMD160 c3b00a7edb9af349f2321fcbbdc286168d5d6db3 SHA1 346cada59b9daea1166fda9fe0b5b34303b0bd6e SHA256 57513d9f897776055dfbe14e717761de314e79409def91ccc27563a613a66e18
-MD5 285e67094e0841a79a32c9301c023b39 files/dont-build-libint.patch 355
-RMD160 c3b00a7edb9af349f2321fcbbdc286168d5d6db3 files/dont-build-libint.patch 355
-SHA256 57513d9f897776055dfbe14e717761de314e79409def91ccc27563a613a66e18 files/dont-build-libint.patch 355
-AUX respect-cflags.patch 464 RMD160 c5323a4944cc953336b70f924ced36aca1533301 SHA1 e6ed80baa01ed807778411760b69e51e969b9601 SHA256 851c738b9ecfa567b21f3b551e6819b8ae05db02a3f5a42ae4aa93d55577ed0e
-MD5 bed0da2f6883825c195e05f8f00e5415 files/respect-cflags.patch 464
-RMD160 c5323a4944cc953336b70f924ced36aca1533301 files/respect-cflags.patch 464
-SHA256 851c738b9ecfa567b21f3b551e6819b8ae05db02a3f5a42ae4aa93d55577ed0e files/respect-cflags.patch 464
-AUX try-more-compilers.patch 401 RMD160 550151b01cc4362d70c3e79d250a2fb2e36af64f SHA1 8b3efe8e30f6ebc6887dc6be60b70faf34b9a188 SHA256 cb3b404ad7725700840df7602686d651f38f3d7623857af63e3556d1317aaf08
-MD5 9ec964134fe443be4a6d6760278bea87 files/try-more-compilers.patch 401
-RMD160 550151b01cc4362d70c3e79d250a2fb2e36af64f files/try-more-compilers.patch 401
-SHA256 cb3b404ad7725700840df7602686d651f38f3d7623857af63e3556d1317aaf08 files/try-more-compilers.patch 401
-AUX try-pthread-for-blas-lapack.patch 1489 RMD160 092e0613b7184b065bb5ffa2288ce342e84d9483 SHA1 97d0802c6d568cb093f9f9c5989dccf4d2abfae6 SHA256 09cf2f5bc6835697322501280de3027b932416dd939d04d0d25a9790fe02eaa5
-MD5 f73030c473338710e13e3dfe3ce59463 files/try-pthread-for-blas-lapack.patch 1489
-RMD160 092e0613b7184b065bb5ffa2288ce342e84d9483 files/try-pthread-for-blas-lapack.patch 1489
-SHA256 09cf2f5bc6835697322501280de3027b932416dd939d04d0d25a9790fe02eaa5 files/try-pthread-for-blas-lapack.patch 1489
-AUX use-external-libint.patch 1359 RMD160 560598e6d7c99d901d97dd6037480bd57c82433f SHA1 4516be3df75ef4fa776655791483f6df823467a5 SHA256 41faa20ba804e98a81cb6809c789c643fd17458b6f6bc95dbe6311dd2fb16713
-MD5 6dc1efc685dfc6994c972eed20daf18c files/use-external-libint.patch 1359
-RMD160 560598e6d7c99d901d97dd6037480bd57c82433f files/use-external-libint.patch 1359
-SHA256 41faa20ba804e98a81cb6809c789c643fd17458b6f6bc95dbe6311dd2fb16713 files/use-external-libint.patch 1359
-DIST poaV2.tar.gz 62612 RMD160 31fdc50527a826fb7fdab4256f51e4f0f03c5492 SHA1 57f863956736498dd76afb57967036bf92c6d599 SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2
-EBUILD poa-2.ebuild 1070 RMD160 4d92c2fba22ff0c5d6a7cc2b9467472cb7277746 SHA1 c01714c7dd0077e06347182c85bfab3b0032a811 SHA256 b3b57857b84088dfc4343da54050e3e894b5dc2cf0cabb1f5980494cf778535d
-MD5 1f51c92e419a9de67795e64866406c5f poa-2.ebuild 1070
-RMD160 4d92c2fba22ff0c5d6a7cc2b9467472cb7277746 poa-2.ebuild 1070
-SHA256 b3b57857b84088dfc4343da54050e3e894b5dc2cf0cabb1f5980494cf778535d poa-2.ebuild 1070
-MD5 c40b5662c1ced482b5071f596493c297 files/digest-poa-2 214
-RMD160 ca39533967c38989bfc8b08772a53dba3d09ce15 files/digest-poa-2 214
-SHA256 034b82fef594cbf7567ceca3fa49e761d5b1654df48056be2d708d63f792127a files/digest-poa-2 214
diff --git a/sci-biology/poa/files/add-libint-error-message.patch b/sci-biology/poa/files/add-libint-error-message.patch
deleted file mode 100644
index 60fb128..0000000
--- a/sci-biology/poa/files/add-libint-error-message.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- psi3.orig/src/lib/libint/Makefile.in	2003-11-23 11:07:51.000000000 -0800
-+++ psi3/src/lib/libint/Makefile.in	2006-02-10 22:38:37.000000000 -0800
-@@ -44,7 +44,10 @@
- $(MAKE) top_objdir=$(top_objdir_path); \
- rm -f Makefile; \
- if ! ./$(BUILD_BINARY); then \
-- cd ..; rm -fR $(TEMP_DIR); exit 1; \
-+ cd ..; \
-+ rm -fR $(TEMP_DIR); \
-+ echo "$(BUILD_BINARY) does not exist!"; \
-+ exit 1; \
- fi; \
- cp Makefile.libint Makefile; \
- ${MAKE} top_objdir=$(top_objdir_path); \
-@@ -65,7 +68,9 @@
- 	$(MKDIRS) $(libdir)
- 	$(INSTALL_DATA) $< $(libdir)
- 	$(RANLIB) $(libdir)/`basename $(TARGET)`
-+	echo Finished ranlib
- 	$(MKDIRS) $(incdir)/libint
-+	echo Finished mkdirs
- 	$(INSTALL_INCLUDE) $(TARGET_HEADERS) $(incdir)/libint
- 
- #
diff --git a/sci-biology/poa/files/digest-dialign-t-0.2.1 b/sci-biology/poa/files/digest-dialign-t-0.2.1
deleted file mode 100644
index fd423eb..0000000
--- a/sci-biology/poa/files/digest-dialign-t-0.2.1
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 d1d4fc381a009c68387e159b78b33801 DIALIGN-T_0.2.1.tar.gz 1635888
-RMD160 a43807668354120b873cad0120a7691b6860ca28 DIALIGN-T_0.2.1.tar.gz 1635888
-SHA256 2249bf9007588e891525b4edc085285f1390c2bf8d42ce327aa9217130d7e930 DIALIGN-T_0.2.1.tar.gz 1635888
diff --git a/sci-biology/poa/files/digest-muscle-3.6 b/sci-biology/poa/files/digest-muscle-3.6
deleted file mode 100644
index 343f62a..0000000
--- a/sci-biology/poa/files/digest-muscle-3.6
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 e721d0859da9feec3cedeb42dcee9f59 muscle3.6_src.tar.gz 185267
-RMD160 4afda92b982ec2b05853a582479c61a7d8814f51 muscle3.6_src.tar.gz 185267
-SHA256 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431 muscle3.6_src.tar.gz 185267
diff --git a/sci-biology/poa/files/digest-poa-2 b/sci-biology/poa/files/digest-poa-2
deleted file mode 100644
index acdb441..0000000
--- a/sci-biology/poa/files/digest-poa-2
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 9e2eb270d4867114406f53dab1311b2b poaV2.tar.gz 62612
-RMD160 31fdc50527a826fb7fdab4256f51e4f0f03c5492 poaV2.tar.gz 62612
-SHA256 d98d8251af558f442d909a6527694825ef6f79881b7636cad4925792559092c2 poaV2.tar.gz 62612
diff --git a/sci-biology/poa/files/digest-probcons-1.10 b/sci-biology/poa/files/digest-probcons-1.10
deleted file mode 100644
index e49b293..0000000
--- a/sci-biology/poa/files/digest-probcons-1.10
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 c7938b95732a85c35225bafd4b5b174f probcons_v1_10.tar.gz 43004
-RMD160 ba7caa3cadd702c3dc00c20f01bfb22416435784 probcons_v1_10.tar.gz 43004
-SHA256 f7a775ac4ba3b3261c0bbe5d2c203c96fc2551e67448aefbac83b461c931b518 probcons_v1_10.tar.gz 43004
diff --git a/sci-biology/poa/files/digest-psi-3.2.3 b/sci-biology/poa/files/digest-psi-3.2.3
deleted file mode 100644
index 00ee001..0000000
--- a/sci-biology/poa/files/digest-psi-3.2.3
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 d304c9510fda1751a988b1e4f619e141 psi-3.2.3.tar.gz 2694286
-RMD160 19bc9a80380193fb3e6d6166f7aa8c98a0415222 psi-3.2.3.tar.gz 2694286
-SHA256 b966c33a82a930b90c1102ade52b7074dd50a9f70a3781d2408436fee68131be psi-3.2.3.tar.gz 2694286
diff --git a/sci-biology/poa/files/dont-build-libint.patch b/sci-biology/poa/files/dont-build-libint.patch
deleted file mode 100644
index 1ad5ce7..0000000
--- a/sci-biology/poa/files/dont-build-libint.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- psi3.orig/src/lib/Makefile.in	2004-01-19 09:09:53.000000000 -0800
-+++ psi3/src/lib/Makefile.in	2006-02-10 21:35:20.000000000 -0800
-@@ -2,7 +2,7 @@
- .PHONY:	default all install depend clean targetclean
- 
- subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd \
--          libint libderiv libr12 libbasis
-+          libbasis
- 
- all: default
- 
diff --git a/sci-biology/poa/files/respect-cflags.patch b/sci-biology/poa/files/respect-cflags.patch
deleted file mode 100644
index 2ae08db..0000000
--- a/sci-biology/poa/files/respect-cflags.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff -urN poaV2.orig/Makefile poaV2/Makefile
---- poaV2.orig/Makefile	2004-03-11 21:33:30.000000000 -0800
-+++ poaV2/Makefile	2006-03-09 20:09:27.000000000 -0800
-@@ -28,7 +28,8 @@
- 
- CC = gcc
- #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
--CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
-+OPT_CFLAGS = -g
-+CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
- # -I$(HOME)/lib/include
- # -DREPORT_MAX_ALLOC
- 
diff --git a/sci-biology/poa/files/try-more-compilers.patch b/sci-biology/poa/files/try-more-compilers.patch
deleted file mode 100644
index 63d4618..0000000
--- a/sci-biology/poa/files/try-more-compilers.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- psi3.orig/configure.in	2005-10-29 10:15:06.000000000 -0700
-+++ psi3/configure.in	2006-02-10 20:56:59.000000000 -0800
-@@ -104,9 +104,9 @@
- ######################
- 
- # potential names of compilers
--FC_LIST="g77 f77 fc f2c"
--CC_LIST="gcc cc"
--CXX_LIST="g++ c++ cxx"
-+FC_LIST="gfortran g77 f77 fc f2c ifc"
-+CC_LIST="gcc cc icc"
-+CXX_LIST="g++ c++ cxx icc"
- 
- # set up os specific options
- case $os in
diff --git a/sci-biology/poa/files/try-pthread-for-blas-lapack.patch b/sci-biology/poa/files/try-pthread-for-blas-lapack.patch
deleted file mode 100644
index d9b01ed..0000000
--- a/sci-biology/poa/files/try-pthread-for-blas-lapack.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- psi3.orig/configure.in	2005-10-29 10:15:06.000000000 -0700
-+++ psi3/configure.in	2006-02-10 20:56:59.000000000 -0800
-@@ -333,7 +333,7 @@
- AC_ARG_WITH(blas,[  --with-blas             which blas library to use],[
- case $withval in
-   yes)
--    BLAS='-lblas'
-+    BLAS='-lblas -lpthread'
-     ;;
-   no)
-     BLAS=''
-@@ -344,16 +344,16 @@
- esac
- ])
- if test "X$BLAS" = X; then
--  AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl")
-+  AC_CHECK_LIB(essl, DGEMM, BLAS="-lessl -lpthread",, [-lpthread])
- fi
- if test "X$BLAS" = X; then
--  AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs")
-+  AC_CHECK_LIB(scs, DGEMM, BLAS="-lscs -lpthread",, [-lpthread])
- fi
- if test "X$BLAS" = X; then
--  AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas")
-+  AC_CHECK_LIB(atlas, DGEMM, BLAS="-latlas -lpthread",, [-lpthread])
- fi
- if test "X$BLAS" = X; then
--  AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas")
-+  AC_CHECK_LIB(blas, DGEMM, BLAS="-lblas -lpthread",, [-lpthread])
- fi
- if test "X$BLAS" = X; then
-  AC_MSG_ERROR("Did not find a BLAS library")
-@@ -363,7 +363,7 @@
- AC_ARG_WITH(lapack,[  --with-lapack           which lapack library to use],[
- case $withval in
-   yes)
--    LAPACK='-llapack'
-+    LAPACK='-llapack -lpthread'
-     ;;
-   no)
-     LAPACK=''
-@@ -382,7 +382,7 @@
-   LIBS=$CURRENT_LIBS
- fi
- if test "X$LAPACK" = X; then
--  AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS)
-+  AC_CHECK_LIB(lapack,DGEEV, LAPACK="-llapack",,$BLAS -lpthread)
- fi
- if test "X$LAPACK" = X; then
-  AC_MSG_ERROR("Did not find a LAPACK library")
diff --git a/sci-biology/poa/files/use-external-libint.patch b/sci-biology/poa/files/use-external-libint.patch
deleted file mode 100644
index 1d9ce91..0000000
--- a/sci-biology/poa/files/use-external-libint.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- psi3.orig/src/bin/cints/Makefile.in	2003-11-14 08:15:19.000000000 -0800
-+++ psi3/src/bin/cints/Makefile.in	2006-02-10 22:42:31.000000000 -0800
-@@ -51,25 +51,25 @@
- # and form the list of the libraries. Remember that libderiv and libr12
- # depend on libint, and hence need to come first for GNU ld to work.
- #
--INTLIBS := -lPSI_int
-+INTLIBS := -lint
- ifeq ($(findstring MP2R12,$(SUBDIRS)),MP2R12)
--  ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12)
--    INTLIBS := -lPSI_r12 $(INTLIBS)
-+  ifneq ($(findstring -lr12,$(INTLIBS)),-lr12)
-+    INTLIBS := -lr12 $(INTLIBS)
-   endif
- endif
- ifeq ($(findstring R12_Ints,$(SUBDIRS)),R12_Ints)
--  ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12)
--    INTLIBS := -lPSI_r12 $(INTLIBS)
-+  ifneq ($(findstring -lr12,$(INTLIBS)),-lr12)
-+    INTLIBS := -lr12 $(INTLIBS)
-   endif
- endif
- ifeq ($(findstring Default_Deriv1,$(SUBDIRS)),Default_Deriv1)
--  ifneq ($(findstring -lPSI_deriv,$(INTLIBS)),-lPSI_deriv)
--    INTLIBS := -lPSI_deriv $(INTLIBS)
-+  ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv)
-+    INTLIBS := -lderiv $(INTLIBS)
-   endif
- endif
- ifeq ($(findstring Default_Deriv2,$(SUBDIRS)),Default_Deriv2)
--  ifneq ($(findstring -lderiv,$(INTLIBS)),-lPSI_deriv)
--    INTLIBS := -lPSI_deriv $(INTLIBS)
-+  ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv)
-+    INTLIBS := -lderiv $(INTLIBS)
-   endif
- endif
- 
diff --git a/sci-biology/poa/poa-2.ebuild b/sci-biology/poa/poa-2.ebuild
deleted file mode 100644
index f466339..0000000
--- a/sci-biology/poa/poa-2.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-misc/colordiff/colordiff-1.0.5-r2.ebuild,v 1.7 2005/08/17 18:08:02 grobian Exp $
-
-inherit eutils
-
-MY_P="${PN}V${PV}"
-DESCRIPTION="Fast multiple sequence alignments using partial-order graphs"
-HOMEPAGE="http://www.bioinformatics.ucla.edu/poa/"
-SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz"
-# According to SF project page
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}"
-S="${WORKDIR}/${MY_P}"
-
-src_unpack() {
-	unpack ${A}
-	epatch "${FILESDIR}"/respect-cflags.patch
-}
-
-src_compile() {
-	emake \
-		OPT_CFLAGS="${CFLAGS}" \
-		poa \
-		|| die "make failed"
-}
-
-src_install() {
-	exeinto /usr/bin
-	doexe "${S}"/poa "${S}"/make_pscores.pl
-	dolib.a "${S}"/liblpo.a
-	dodoc "${S}"/README "${S}"/multidom.*
-	insinto /usr/share/poa
-	doins "${S}"/*.mat
-}
-
-pkg_postinst() {
-	elog "poa requires a score matrix as the first argument."
-	elog "This package installs two examples to ${ROOT}usr/share/poa/."
-}