diff options
author | Donnie Berkholz <dberkholz@gentoo.org> | 2006-10-20 23:32:13 -0700 |
---|---|---|
committer | Donnie Berkholz <dberkholz@gentoo.org> | 2006-10-20 23:32:13 -0700 |
commit | 9efbe945a14a441a171e9634718c3435c9ca92ea (patch) | |
tree | 9b5d00f3ecd1a73ef557d9a34ea26b6bccaded38 /sci-biology | |
parent | poa: final QA checks for main tree (diff) | |
download | dberkholz-9efbe945a14a441a171e9634718c3435c9ca92ea.tar.gz dberkholz-9efbe945a14a441a171e9634718c3435c9ca92ea.tar.bz2 dberkholz-9efbe945a14a441a171e9634718c3435c9ca92ea.zip |
poa: merged to gentoo-x86
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/poa/Manifest | 32 | ||||
-rw-r--r-- | sci-biology/poa/files/add-libint-error-message.patch | 24 | ||||
-rw-r--r-- | sci-biology/poa/files/digest-dialign-t-0.2.1 | 3 | ||||
-rw-r--r-- | sci-biology/poa/files/digest-muscle-3.6 | 3 | ||||
-rw-r--r-- | sci-biology/poa/files/digest-poa-2 | 3 | ||||
-rw-r--r-- | sci-biology/poa/files/digest-probcons-1.10 | 3 | ||||
-rw-r--r-- | sci-biology/poa/files/digest-psi-3.2.3 | 3 | ||||
-rw-r--r-- | sci-biology/poa/files/dont-build-libint.patch | 11 | ||||
-rw-r--r-- | sci-biology/poa/files/respect-cflags.patch | 13 | ||||
-rw-r--r-- | sci-biology/poa/files/try-more-compilers.patch | 15 | ||||
-rw-r--r-- | sci-biology/poa/files/try-pthread-for-blas-lapack.patch | 50 | ||||
-rw-r--r-- | sci-biology/poa/files/use-external-libint.patch | 37 | ||||
-rw-r--r-- | sci-biology/poa/poa-2.ebuild | 44 |
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/." -} |