From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 3D13F1580B1 for ; Tue, 31 Aug 2021 09:24:15 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 430D6E095C; Tue, 31 Aug 2021 09:24:13 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 9D19CE088B for ; Tue, 31 Aug 2021 09:24:11 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 99E7B33EDD8 for ; Tue, 31 Aug 2021 09:24:10 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 23D0290 for ; Tue, 31 Aug 2021 09:24:09 +0000 (UTC) From: "Andrew Ammerlaan" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" Message-ID: <1630401568.f5bcc5911aea4f5c5cb38e65c8bc1a01fbc6bcf2.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/cgview-bin/ X-VCS-Repository: proj/sci X-VCS-Files: profiles/package.mask sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild sci-biology/cgview-bin/metadata.xml X-VCS-Directories: profiles/ sci-biology/cgview-bin/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: f5bcc5911aea4f5c5cb38e65c8bc1a01fbc6bcf2 X-VCS-Branch: master Date: Tue, 31 Aug 2021 09:24:09 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 62febc19-bb62-4cdf-bc04-d60e8287ab56 X-Archives-Hash: 489ca18de06a018656084d4c9f91fee5 commit: f5bcc5911aea4f5c5cb38e65c8bc1a01fbc6bcf2 Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Aug 31 09:19:28 2021 +0000 Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Aug 31 09:19:28 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f5bcc591 sci-biology/cgview-bin: remove last-rited pack Signed-off-by: Andrew Ammerlaan gentoo.org> profiles/package.mask | 1 - sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild | 43 -------------------------- sci-biology/cgview-bin/metadata.xml | 12 ------- 3 files changed, 56 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index a58bd71ee..83a94e897 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -37,7 +37,6 @@ # Bug #798015, removal in 30 days. # Perhaps these packages work with the newer ncbi-tools++? If anyone is actively # using these packages please open a bug report -sci-biology/cgview-bin sci-biology/prot4EST sci-biology/seqclean sci-chemistry/talosn diff --git a/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild b/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild deleted file mode 100644 index 5135e04ab..000000000 --- a/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 perl-module eutils toolchain-funcs - -DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)" -HOMEPAGE="https://paulstothard.github.io/cgview_comparison_tool/" -SRC_URI="https://github.com/paulstothard/cgview_comparison_tool/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - >=dev-lang/perl-5.8.8 - >=sci-biology/ncbi-tools-2.2.15 - >=virtual/jre-1.4.2:* - dev-java/xerces:2 - dev-java/batik - dev-java/commons-lang:2.1 - >=media-gfx/imagemagick-6 - >=sci-biology/bioperl-1.4.0" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/cgview_comparison_tool-${PV}" - -src_install() { - insinto /usr/share/${PN}/scripts - chmod a+x scripts/* # BUG: this does not work - doins -r scripts/* - insinto /usr/share/${PN}/lib/scripts - doins -r lib/scripts/* - echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview' > "${S}/99cgview" - echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview" - doenvd "${S}/99cgview" - perl_set_version - perl_domodule lib/perl_modules/Util/*.pm - # - # Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2DIOException - java-pkg_dojar bin/cgview/cgview.jar -} diff --git a/sci-biology/cgview-bin/metadata.xml b/sci-biology/cgview-bin/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/cgview-bin/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - mmokrejs@fold.natur.cuni.cz - Martin Mokrejs - - - sci-biology@gentoo.org - Gentoo Biology Project - -