[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/estscan/

[Andrew Ammerlaan]

commit:     9c80f0ef473bca66c7cbd29c41a7330958f8d820
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Dec  1 21:55:13 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Dec  1 21:55:50 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c80f0ef

sci-biology/estscan: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.use.mask                |   4 -
 sci-biology/estscan/estscan-3.0.3.ebuild | 124 -------------------------------
 sci-biology/estscan/metadata.xml         |  19 -----
 3 files changed, 147 deletions(-)

diff --git a/profiles/package.use.mask b/profiles/package.use.mask
index 8aff1df94..b4116bd86 100644
--- a/profiles/package.use.mask
+++ b/profiles/package.use.mask
@@ -23,10 +23,6 @@ sci-libs/gdcm python
 # doesn't link with plotutils-2.6
 sci-physics/qcl plotutils
 
-# Christoph Junghans <ottxor@g.o> (12 Sep 2014)
-# icc and ifc don't work on no-multilib
-sci-biology/estscan icc ifc
-
 # Christoph Junghans <ottxor@g.o> (05 Nov 2013)
 # gui sandbox error
 dev-lang/conceptual gui

diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild
deleted file mode 100644
index a0992b76b..000000000
--- a/sci-biology/estscan/estscan-3.0.3.ebuild
+++ /dev/null
@@ -1,124 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit fortran-2 perl-module toolchain-funcs
-
-DESCRIPTION="Prediction of coding regions in DNA/RNA sequences"
-HOMEPAGE="https://sourceforge.net/projects/estscan/"
-SRC_URI="
-	https://downloads.sourceforge.net/${PN}/${P}.tar.gz
-	https://downloads.sourceforge.net/${PN}/At.smat.gz
-	https://downloads.sourceforge.net/${PN}/Dm.smat.gz
-	https://downloads.sourceforge.net/${PN}/Dr.smat.gz
-	https://downloads.sourceforge.net/${PN}/Hs.smat.gz
-	https://downloads.sourceforge.net/${PN}/Mm.smat.gz
-	https://downloads.sourceforge.net/${PN}/Rn.smat.gz
-	https://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf
-	https://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz"
-
-SLOT="0"
-LICENSE="estscan"
-KEYWORDS="~amd64 ~x86"
-IUSE="icc ifc"
-
-DEPEND="
-	dev-perl/BTLib
-	icc? ( dev-lang/icc )
-	ifc? ( dev-lang/ifc )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	default
-	sed \
-		-e 's/\\rm -f/rm -rf/' \
-		-e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \
-		-i "${P}"/Makefile || die "failed to edit Makefile"
-
-	# fix hard-coded paths
-	sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.c || die
-	sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.spec || die
-
-	if ! use icc; then
-		sed \
-			-e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' -i "${P}"/Makefile || die
-	fi
-
-	if ! use ifc; then
-		sed \
-			-e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \
-			-e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \
-			|| die
-	fi
-
-	if use icc; then
-		# FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives
-		# me gcc instead, same for $(tc-getF77)
-		# Moreover, the if/else logic here should separate users having only icc
-		# while not ifort (and vice-versa) from those having only
-		# gcc/gfortran/g77
-		#
-		# FIXME: below as a dirty hack I force gfortran instead of ifort for
-		# my testing purposes. Didn't ebuild contain "PROVIDES" line?
-		# Same for FFLAGS.
-		sed \
-			-e "s:^# CC = icc:CC = icc:" \
-			-e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \
-			-e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \
-			-e "s/^ CC = gcc/# CC = gcc/" \
-			-i "${P}"/Makefile || die "sed failed to fix CFLAGS and CC"
-
-	fi
-
-	if use ifc; then
-		sed \
-			-e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \
-			-e "s/^# F77 = ifort/F77 = gfortran/" \
-			-e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \
-			-e "s/^ F77 = g77/# F77 = g77/" \
-			-i "${P}"/Makefile || die "sed failed to fix FFLAGS and F77"
-	fi
-}
-
-src_compile() {
-	emake -C ${P}
-}
-
-src_install() {
-	# FIXME: Some kind of documentation is in {P}/${PN}.spec
-	cd ${P} || die "Failed to chdir to ${P}"
-	dobin \
-		build_model ${PN} evaluate_model extract_EST extract_UG_EST \
-		extract_mRNA makesmat maskred prepare_data winsegshuffle
-	# the file build_model_utils.pl should go into some PERL site-packages dir
-	# see {P}/${PN}.spec
-
-	# install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension
-	insinto /usr/share/doc/${PN}
-	# grab the file directly from ../distdir/
-	doins "${DISTDIR}"/user_guide_fev_07.pdf
-
-	# install the default precomputed matrices
-	cd "${WORKDIR}" || die "Failed to chdir to ${WORKDIR}"
-	insinto /usr/share/${PN}
-	doins *.smat
-
-	# install BTlib (in perl)
-	# dobin fetch indexer netfetch
-	insinto /usr/share/${PN}/
-	# install the config file which is packed inside the BTLib tarball while is not
-	# being installed by dev-perl/BTLib
-	doins "${WORKDIR}"/BTLib-0.19/fetch.conf
-
-	# FIXME: install the *.pm files from BTLib-0.19
-	# cd "${WORKDIR}"/BTLib-0.19 || die "Failed to chdir to "${WORKDIR}"/BTLib-0.19
-	# myinst="DESTDIR=${D}"
-	# perl-module_src_install
-
-	einfo "Please edit /usr/share/${PN}/fetch.conf to fit your local database layout."
-	einfo "Also create your own scoring matrices and place them into /usr/share/${PN}/."
-	einfo "You may follow the hints from http://${PN}.sourceforge.net/"
-}

diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml
deleted file mode 100644
index c79c2d1b5..000000000
--- a/sci-biology/estscan/metadata.xml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@×××××××××××××××.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@g.o</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<use>
-		<flag name="icc">Undocumented USE</flag>
-		<flag name="ifc">Undocumented USE</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>