From 5781aaa8b6bccd389d6520199e68819a84969412 Mon Sep 17 00:00:00 2001 From: Jakov Smolić Date: Mon, 30 Aug 2021 19:15:43 +0200 Subject: sci-biology/psipred: Remove last-rited package MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jakov Smolić --- 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 ---------------------------- 6 files changed, 155 deletions(-) delete mode 100644 sci-biology/psipred/Manifest delete mode 100644 sci-biology/psipred/files/3.1-Makefile.patch delete mode 100644 sci-biology/psipred/files/3.1-path.patch delete mode 100644 sci-biology/psipred/files/3.2-fgets.patch delete mode 100644 sci-biology/psipred/metadata.xml delete mode 100644 sci-biology/psipred/psipred-3.5.ebuild (limited to 'sci-biology') diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest deleted file mode 100644 index e16749782317..000000000000 --- 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 0c70b6868565..000000000000 --- 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 564e9c8a1ef9..000000000000 --- 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 = $basename:t diff --git a/sci-biology/psipred/files/3.2-fgets.patch b/sci-biology/psipred/files/3.2-fgets.patch deleted file mode 100644 index ec06d141ee34..000000000000 --- a/sci-biology/psipred/files/3.2-fgets.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c -index 37b1332..4f04ab6 100644 ---- a/src/sspred_avpred.c -+++ b/src/sspred_avpred.c -@@ -223,7 +223,7 @@ predict(int argc, char **argv) - int getmtx(FILE *lfil) - { - int aa, i, j, naa; -- char buf[256], *p; -+ char buf[65536], *p; - - if (fscanf(lfil, "%d", &naa) != 1) - fail("Bad mtx file - no sequence length!"); diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml deleted file mode 100644 index 959160fe46b1..000000000000 --- a/sci-biology/psipred/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - diff --git a/sci-biology/psipred/psipred-3.5.ebuild b/sci-biology/psipred/psipred-3.5.ebuild deleted file mode 100644 index f5619ef4b544..000000000000 --- a/sci-biology/psipred/psipred-3.5.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit epatch prefix toolchain-funcs versionator - -#MY_P="${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" -} -- cgit v1.2.3-65-gdbad