[gentoo-commits] repo/gentoo:master commit in: sci-biology/psipred/files/, sci-biology/psipred/, profiles/

[Jakov Smolić]

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 <dilfridge@g.o> (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-biology@g.o</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"
-}