commit: 5781aaa8b6bccd389d6520199e68819a84969412
Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 30 17:15:43 2021 +0000
Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
CommitDate: Mon Aug 30 17:38:48 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5781aaa8
sci-biology/psipred: Remove last-rited package
Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org>
profiles/package.mask | 1 -
sci-biology/psipred/Manifest | 2 -
sci-biology/psipred/files/3.1-Makefile.patch | 38 -------------------
sci-biology/psipred/files/3.1-path.patch | 38 -------------------
sci-biology/psipred/files/3.2-fgets.patch | 13 -------
sci-biology/psipred/metadata.xml | 8 ----
sci-biology/psipred/psipred-3.5.ebuild | 56 ----------------------------
7 files changed, 156 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 9a9c7dde826..484e5b1182a 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -286,7 +286,6 @@ sci-libs/sktime
# Bug #798015, removal in 30 days.
sci-biology/ncbi-tools
sci-biology/njplot
-sci-biology/psipred
# Andreas K. Hüttel <dilfri...@gentoo.org> (2021-07-31)
# Obsolete; all versions in current Perl core distributions
diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
deleted file mode 100644
index e1674978231..00000000000
--- a/sci-biology/psipred/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST psipred3.5.tar.gz 1101579 BLAKE2B
2fd86841cbc4bb86045b51f8283550832df8356ee88a6ef2c85281b5810debb23ac53652ddc5ffc9bd6f8e9e7248ce39ccee23400ff8fb49cd05b877d730b553
SHA512
a7b3f7d149f6a29cf0b48bdb900f6983d42af01132d8b54a7be88994d09fcf27dbe57115d41ec9654da6daf6898d5986d08fbdcefa3a4c81af0d358500cd40c2
-DIST tdbdata.tar.gz 40241247 BLAKE2B
c85a2fde9b29a14e1da27be1a7ea5fe1704f72b66cd79514dd50a3a0d2d8aab9341f7d5075f6d1896cefa54ca83948387b902b38780181777dc505a9a15b4aab
SHA512
f96d7ffbb77e129251e27f62b7f099d944bacd14935e03fc52c9f0b262cce1ad477ad43520a93b407951fb8f5dd3ba2e27ff6b5ae8a637ec03bc02f8c7c3990c
diff --git a/sci-biology/psipred/files/3.1-Makefile.patch
b/sci-biology/psipred/files/3.1-Makefile.patch
deleted file mode 100644
index 0c70b686856..00000000000
--- a/sci-biology/psipred/files/3.1-Makefile.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff --git a/src/Makefile b/src/Makefile
-index abed8af..26061fa 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -6,9 +6,9 @@
- #### CFLAGS Flags to pass to C compiler.
-
- INCDIR = .
--CC = cc
-+CC ?= gcc
-
--CFLAGS = -O
-+CFLAGS ?= -O2
- LIBS = -lm
-
- all: psipred psipass2 chkparse seq2mtx pfilt
-@@ -20,16 +20,16 @@ clean:
- /bin/rm -f psipred psipass2 chkparse seq2mtx pfilt
-
- psipred: sspred_avpred.c ssdefs.h sspred_net.h
-- $(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred
-+ $(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred
-
- psipass2: sspred_hmulti.c ssdefs.h sspred_net2.h
-- $(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
-+ $(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
-
- chkparse: chkparse.c
-- $(CC) $(CFLAGS) chkparse.c $(LIBS) -o chkparse
-+ $(CC) $(CFLAGS) $(LDFLAGS) chkparse.c $(LIBS) -o chkparse
-
- seq2mtx: seq2mtx.c
-- $(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
-+ $(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
-
- pfilt: pfilt.c
-- $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt
-+ $(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt
diff --git a/sci-biology/psipred/files/3.1-path.patch
b/sci-biology/psipred/files/3.1-path.patch
deleted file mode 100644
index 564e9c8a1ef..00000000000
--- a/sci-biology/psipred/files/3.1-path.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff --git a/runpsipred b/runpsipred
-index 4ccf44e..34dee99 100755
---- a/runpsipred
-+++ b/runpsipred
-@@ -14,13 +14,13 @@
- set dbname = uniref90filt
-
- # Where the NCBI programs have been installed
--set ncbidir = /usr/local/bin
-+set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
-
- # Where the PSIPRED V2 programs have been installed
--set execdir = ./bin
-+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
-
- # Where the PSIPRED V2 data files have been installed
--set datadir = ./data
-+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
-
- set basename = $1:r
- set rootname = $basename:t
-diff --git a/runpsipred_single b/runpsipred_single
-index 1f7680b..7bd5bc3 100755
---- a/runpsipred_single
-+++ b/runpsipred_single
-@@ -10,10 +10,10 @@
- # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
-
- # Where the PSIPRED V3 programs have been installed
--set execdir = ./bin
-+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
-
- # Where the PSIPRED V3 data files have been installed
--set datadir = ./data
-+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
-
- set basename = $1:r
- set rootname = $basename:t
diff --git a/sci-biology/psipred/files/3.2-fgets.patch
b/sci-biology/psipred/files/3.2-fgets.patch
deleted file mode 100644
index ec06d141ee3..00000000000
--- a/sci-biology/psipred/files/3.2-fgets.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c
-index 37b1332..4f04ab6 100644
---- a/src/sspred_avpred.c
-+++ b/src/sspred_avpred.c
-@@ -223,7 +223,7 @@ predict(int argc, char **argv)
- int getmtx(FILE *lfil)
- {
- int aa, i, j, naa;
-- char buf[256], *p;
-+ char buf[65536], *p;
-
- if (fscanf(lfil, "%d", &naa) != 1)
- fail("Bad mtx file - no sequence length!");
diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml
deleted file mode 100644
index 959160fe46b..00000000000
--- a/sci-biology/psipred/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biol...@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/psipred/psipred-3.5.ebuild
b/sci-biology/psipred/psipred-3.5.ebuild
deleted file mode 100644
index f5619ef4b54..00000000000
--- a/sci-biology/psipred/psipred-3.5.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit epatch prefix toolchain-funcs versionator
-
-#MY_P="${PN}$(delete_all_version_separators)"
-MY_P="${PN}${PV}"
-
-DESCRIPTION="Protein Secondary Structure Prediction"
-HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/";
-SRC_URI="
- http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
- test? (
http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
-
-LICENSE="psipred"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- app-shells/tcsh
- sci-biology/ncbi-tools
- sci-biology/update-blastdb"
-DEPEND=""
-
-S="${WORKDIR}"/${PN}
-
-src_prepare() {
- rm -f bin/*
- epatch \
- "${FILESDIR}"/3.1-Makefile.patch \
- "${FILESDIR}"/3.1-path.patch \
- "${FILESDIR}"/3.2-fgets.patch
- eprefixify runpsipred*
- emake -C src clean
-}
-
-src_compile() {
- emake -C src CC=$(tc-getCC)
-}
-
-src_install() {
- emake -C src DESTDIR="${D}" install
- dobin runpsipred* bin/* BLAST+/runpsipred*
- insinto /usr/share/${PN}
- doins -r data
- dodoc README
-}
-
-pkg_postinst() {
- elog "Please use the update_blastdb.pl in order to"
- elog "maintain your own local blastdb"
-}
