* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/, sci-biology/fasta/files/
@ 2018-01-01 12:43 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2018-01-01 12:43 UTC (permalink / raw
To: gentoo-commits
commit: a41c01197596738c1f3af00bda7e3cbf52bc9f1c
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 1 12:42:45 2018 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Jan 1 12:42:45 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a41c0119
sci-biology/fasta: Remove old
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/fasta/Manifest | 1 -
sci-biology/fasta/fasta-35.4.10.ebuild | 57 ---------------------------
sci-biology/fasta/files/35.4.10-ldflags.patch | 26 ------------
3 files changed, 84 deletions(-)
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index 847e1f925c0..800c5b2628b 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,2 +1 @@
-DIST fasta-35.4.10.tar.gz 618971 BLAKE2B cbc413c13f7d5151add9886eb0fbe1d55d9b1847f406ff8fe614e729c6c3ab155711b6c38a2085eabd3f27506562a98ca8d9f1409525f27fe091b30f3a1e840d SHA512 f04268f0eea59cd40985c86597ab68bef40ee28e6ca914a7182c0edfe943ec8fb2a860558f422f210a4c03f3c34f36c677bd3971bc240cb87695826c755f5a47
DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812
diff --git a/sci-biology/fasta/fasta-35.4.10.ebuild b/sci-biology/fasta/fasta-35.4.10.ebuild
deleted file mode 100644
index 8cad4d2a8b0..00000000000
--- a/sci-biology/fasta/fasta-35.4.10.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="2"
-
-inherit eutils flag-o-matic toolchain-funcs
-
-DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz"
-
-LICENSE="fasta"
-SLOT="0"
-KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="debug cpu_flags_x86_sse2 test"
-
-DEPEND="test? ( app-shells/tcsh )"
-RDEPEND=""
-
-src_prepare() {
- CC_ALT=
- CFLAGS_ALT=
- ALT=
-
- use debug && append-flags -DDEBUG
-
- if [[ $(tc-getCC) == *icc* ]]; then
- CC_ALT=icc
- ALT="${ALT}_icc"
- else
- CC_ALT=$(tc-getCC)
- use x86 && ALT="32"
- use amd64 && ALT="64"
- fi
-
- if use cpu_flags_x86_sse2 ; then
- ALT="${ALT}_sse2"
- append-flags -msse2
- [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
- fi
-
- export CC_ALT="${CC_ALT}"
- export ALT="${ALT}"
-
- epatch "${FILESDIR}"/${PV}-ldflags.patch
-}
-
-src_compile() {
- cd src
- emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all || die
-}
-
-src_install() {
- dobin bin/* || die
- doman doc/{prss3.1,fasta35.1,pvcomp.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} || die
- dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} || die
-}
diff --git a/sci-biology/fasta/files/35.4.10-ldflags.patch b/sci-biology/fasta/files/35.4.10-ldflags.patch
deleted file mode 100644
index c3b7a9b5690..00000000000
--- a/sci-biology/fasta/files/35.4.10-ldflags.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-diff --git a/make/Makefile.pcom b/make/Makefile.pcom
-index a808667..405be95 100644
---- a/make/Makefile.pcom
-+++ b/make/Makefile.pcom
-@@ -274,16 +274,16 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
- $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
-
- map_db : map_db.c uascii.h ncbl2_head.h
-- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
-+ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
-
- list_db : list_db.c
-- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
-+ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
-
- lav2ps : lav2plt.o lavplt_ps.o
-- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-+ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-
- lav2svg : lav2plt.o lavplt_svg.o
-- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
-+ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
-
- res_stats : res_stats.o scale_se.o
-- $(CC) -DUNIX -o $(BIN)/res_stats res_stats.o scale_se.o -lm
-+ $(CC) -DUNIX $(HFLAGS) $(BIN)/res_stats res_stats.o scale_se.o -lm
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/fasta/, sci-biology/fasta/files/
@ 2022-03-19 17:08 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2022-03-19 17:08 UTC (permalink / raw
To: gentoo-commits
commit: 5d5c2e0b0e7e7bf0a1a79187db493ba0095d414d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 19 17:07:58 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 19 17:07:58 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5d5c2e0b
sci-biology/fasta: drop 36.3.5e
Closes: https://bugs.gentoo.org/648618
Closes: https://bugs.gentoo.org/828700
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/fasta/Manifest | 1 -
sci-biology/fasta/fasta-36.3.5e.ebuild | 79 ----------------------
.../fasta/files/fasta-36.3.5e-ldflags.patch | 74 --------------------
3 files changed, 154 deletions(-)
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index cff190468270..c0bd97106d3a 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,2 +1 @@
-DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812
DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391
diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild
deleted file mode 100644
index c4c94d0e7f21..000000000000
--- a/sci-biology/fasta/fasta-36.3.5e.ebuild
+++ /dev/null
@@ -1,79 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit epatch flag-o-matic toolchain-funcs
-
-DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
-
-LICENSE="fasta"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="debug cpu_flags_x86_sse2 test"
-RESTRICT="!test? ( test )"
-
-DEPEND="test? ( app-shells/tcsh )"
-RDEPEND=""
-
-src_prepare() {
- CC_ALT=
- CFLAGS_ALT=
- ALT=
-
- use debug && append-flags -DDEBUG
-
- if [[ $(tc-getCC) == *icc* ]]; then
- CC_ALT=icc
- ALT="${ALT}_icc"
- else
- CC_ALT=$(tc-getCC)
- use x86 && ALT="32"
- use amd64 && ALT="64"
- fi
-
- if use cpu_flags_x86_sse2 ; then
- ALT="${ALT}_sse2"
- append-flags -msse2
- [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
- fi
-
- export CC_ALT="${CC_ALT}"
- export ALT="${ALT}"
-
- epatch "${FILESDIR}"/${P}-ldflags.patch
-
- sed \
- -e 's:-ffast-math::g' \
- -i make/Makefile* || die
-
-}
-
-src_compile() {
- cd src || die
- emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
-}
-
-src_test() {
- cd test || die
- FASTLIBS="../conf" bash test.sh || die
-}
-
-src_install() {
- local bin
- dobin bin/*
-
- pushd bin > /dev/null || die
- for bin in *36; do
- dosym ${bin} /usr/bin/${bin%36}
- done
- popd
-
- insinto /usr/share/${PN}
- doins -r conf/* data seq
-
- doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
- dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*}
-}
diff --git a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
deleted file mode 100644
index a6eeabfdf46c..000000000000
--- a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
+++ /dev/null
@@ -1,74 +0,0 @@
- make/Makefile.pcom | 8 ++++----
- make/Makefile.pcom_s | 8 ++++----
- make/Makefile.pcom_t | 8 ++++----
- 3 files changed, 12 insertions(+), 12 deletions(-)
-
-diff --git a/make/Makefile.pcom b/make/Makefile.pcom
-index 9c5f801..33fc001 100644
---- a/make/Makefile.pcom
-+++ b/make/Makefile.pcom
-@@ -209,14 +209,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
- $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
-
- map_db : map_db.c uascii.h ncbl2_head.h
-- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
-+ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
-
- list_db : list_db.c
-- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
-+ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
-
-
- lav2ps : lav2plt.o lavplt_ps.o
-- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-+ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-
- lav2svg : lav2plt.o lavplt_svg.o
-- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
-+ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
-diff --git a/make/Makefile.pcom_s b/make/Makefile.pcom_s
-index dc53001..8a45044 100644
---- a/make/Makefile.pcom_s
-+++ b/make/Makefile.pcom_s
-@@ -143,14 +143,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
- $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
-
- map_db : map_db.c uascii.h ncbl2_head.h
-- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
-+ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
-
- list_db : list_db.c
-- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
-+ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
-
-
- lav2ps : lav2plt.o lavplt_ps.o
-- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-+ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-
- lav2svg : lav2plt.o lavplt_svg.o
-- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
-+ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
-diff --git a/make/Makefile.pcom_t b/make/Makefile.pcom_t
-index 8a71438..5b08a50 100644
---- a/make/Makefile.pcom_t
-+++ b/make/Makefile.pcom_t
-@@ -164,14 +164,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
- $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
-
- map_db : map_db.c uascii.h ncbl2_head.h
-- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
-+ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
-
- list_db : list_db.c
-- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
-+ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
-
-
- lav2ps : lav2plt.o lavplt_ps.o
-- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-+ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
-
- lav2svg : lav2plt.o lavplt_svg.o
-- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
-+ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
^ permalink raw reply related [flat|nested] 2+ messages in thread
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