sci-biology/estscan: treeclean

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

4 files changed, 0 insertions, 156 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@gentoo.org> (12 Sep 2014)
-# icc and ifc don't work on no-multilib
-sci-biology/estscan icc ifc
-
 # Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013)
 # gui sandbox error
 dev-lang/conceptual gui
diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest
deleted file mode 100644
index 79281bc74..000000000
--- a/sci-biology/estscan/Manifest
+++ /dev/null
@@ -1,9 +0,0 @@
-DIST At.smat.gz 32314 BLAKE2B c48c043fa7e7e26e406a677587380e0ade911aafb5878988668da9b9f09a978a369e636c931d2d4d65b6efc65398723e1a78c032805cfc71f2927a42d87788c4 SHA512 aeb3dec65b730570d70e8f49930bf85cc73fe39696d2ccc08e6a804cfe435ea43423f1f4a02b192c68da03727b628bb43ec0ba27bb4549e59f743eccd203df09
-DIST BTLib-0.19.tar.gz 36283 BLAKE2B 53d26fdc7fee3325104a7f2041617bbde464421c540b29c7d47381c60d8f837601e7274d9f0ef5694d1b86b3e2cc7e9a0b289090c3c957a343542e3e7305cd50 SHA512 00261daa7fab4d16dec9e9d4f9e382cc804a10c0ed6b813d6223902b53f6b260dc0a242acfab93897afa750e949ab3f21ecae537206d81eb712f06289387f7d2
-DIST Dm.smat.gz 31711 BLAKE2B 5e8da0668d0788ce2e70535605cb85ced4ec052c4e736b11d838919c0328c6978170aed8e6102d62c6f8770a99a7f49aad373492ddc79328df3238486b7ee703 SHA512 fe141598291fd1bead1f0918c2e52533db1f5c5f60d4c71838a16298ccf60a8a1857a02379f58979dbab3cfad4e0ac64556cf629fcb65d9a0e6861fe4ca163a4
-DIST Dr.smat.gz 8813 BLAKE2B 465d980cc9c1d61f8a83e4c3dd203852b2cfa4bde5730de268655d7a05db9d018f6cff6357246bbfc42002f3993aebf44c9fc27c2d31fa6657194600e5a364b0 SHA512 1880981db252ed08a762fdc8a321b27063ea2341cde56c40146cc7eeed0fdfa620e9b4c71c245fffee6521ae1efbc89b52e6558cd84aef89138e8b26b60460de
-DIST Hs.smat.gz 62935 BLAKE2B 4089dbcc54af5544071d9fc270a9048c758fef15e4846f92dc9c61abd5c60ba9d8ba4a25b9064f4d418cbe1a8a277c5bba49af9a85f51dd9f3bcaac30a7b568d SHA512 7ac3af9b018992014643fbbd83abc4128df4c8b9c516fb1b6b16e1fdc65b23df07811fa5b23ecec5ef2993de71e3efaec5bee3fc1626bcf2984794f13e343447
-DIST Mm.smat.gz 62711 BLAKE2B c65aeb6f8833e4effb360de29e3c25985184e4a9822272f370fc292ec2142843b78ac66485ec98b017aac3a18b7936fc45b510f58cb2db909d5230291573bdf3 SHA512 4ee5fac326bee7e4fe17ad9eab608a90007485a90b479557a181eb49628ff5fee22d04a3ef360b6bc29a76709723faa0a9df8ef1cdb40421d772a0b2dc9f3fc5
-DIST Rn.smat.gz 32388 BLAKE2B 06144cce26cd35eeb15d94db5f169a9cf6c6ab02b4c4f213e42140b2fe864473e7c107c910092620f255384eadd1e07a366e58a21d3df570e63e2843e537aaa3 SHA512 e517d95aa4d1928f766ac9cc885f277d9f980d27265dcc7a2c5d747b1023a5606bccb2dbce2fa9ff76fc0f0333fadd3bc0b7abe9ea4aa82396b57bb06b8dcf43
-DIST estscan-3.0.3.tar.gz 46412 BLAKE2B 998f4f117503e044492495d52e5b064fcb62c3800adb4ec4b357042ea90d8c6ce86902257e5b28ee119c2b332044389c8775101bad6875cba069db6961f73931 SHA512 d3ddb91a71a700a67807a63f7b9c9e2a1c45af847a7808afd757f60f276f7410e22adde6e0ffadbfef8e579890b79fe785b8a05e28cb3d67345464cd2035f69c
-DIST user_guide_fev_07.pdf 327005 BLAKE2B 5d66466c122c12618c5aadb2f12a404159b553b57e80fa421d707d8c3e70d795da7285a6976beacd67b7c6462297fde7843b89b48ed773752cdc0e00bfd1c36c SHA512 de1f046656c3e01a9b3e3930aadc7a91cb10d907a9d6af8fc1c2b0abe6ef0d1305baaeee463c80df0c700951a03b1c26a211fdd14e76fbf41ac5fca3467e49c1
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@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</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>