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 4CD51138806 for ; Mon, 25 Dec 2017 16:09:50 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 57E61E0EEC; Mon, 25 Dec 2017 16:09:49 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (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 28EA5E0EEC for ; Mon, 25 Dec 2017 16:09:48 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (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 55B7433BF24 for ; Mon, 25 Dec 2017 16:09:47 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 94FDCAE96 for ; Mon, 25 Dec 2017 16:09:45 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1514218147.f1a2182baa171c729f5c2134144664780e041f37.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/t-coffee/, sci-biology/t-coffee/files/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/t-coffee/Manifest sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch sci-biology/t-coffee/t-coffee-11.00-r1.ebuild sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild X-VCS-Directories: sci-biology/t-coffee/files/ sci-biology/t-coffee/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: f1a2182baa171c729f5c2134144664780e041f37 X-VCS-Branch: master Date: Mon, 25 Dec 2017 16:09:45 +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-Archives-Salt: 57c8bf2b-d00b-4acb-b464-872947f153f5 X-Archives-Hash: 37bd1ccf79d2df225eb0cedeeba416dd commit: f1a2182baa171c729f5c2134144664780e041f37 Author: David Seifert gentoo org> AuthorDate: Mon Dec 25 10:02:15 2017 +0000 Commit: David Seifert gentoo org> CommitDate: Mon Dec 25 16:09:07 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f1a2182b sci-biology/t-coffee: Remove old Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/t-coffee/Manifest | 2 - .../t-coffee/files/t-coffee-9.03.1318-flags.patch | 21 -------- sci-biology/t-coffee/t-coffee-11.00-r1.ebuild | 56 ---------------------- sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild | 56 ---------------------- 4 files changed, 135 deletions(-) diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest index fab971d3109..447e1125949 100644 --- a/sci-biology/t-coffee/Manifest +++ b/sci-biology/t-coffee/Manifest @@ -1,3 +1 @@ DIST T-COFFEE_distribution_Version_11.00.4466924.tar.gz 3502302 BLAKE2B 0d8087eb219ff72e6f478a779ccdb51e7aee861236c522dec5391e854b0b0bf6eab324009686237e6d334d2e13e17700f6692333060a2ed55711380ef2ab2cdb SHA512 c6c1a7b768156f8457dc4c53a77b14ce0b85e591d60762faf6e6f6f3b60dab75e99449d55b42ef3af1c90e244f735e19abb72d0ce871bb9fbfbb8d1641531293 -DIST T-COFFEE_distribution_Version_11.00.8cbe486.tar.gz 3526354 BLAKE2B fd03894106d09bb95c44fc4f934f99fa6f0b82c56ee9832da2537ebffc12fc9d6e71f1d0371374f397b36852ba85991efb7bdfcc1102737113a35e7943268f68 SHA512 5c486411bae430cfca6f4623f4dff348e2d9ab7c2eb0edef8059c6cb9c01ee48347e06be0c5d19ee1ace4b9f597f19beee8da2d7eecba29c5a78c2aec800be92 -DIST T-COFFEE_distribution_Version_9.03.r1318.tar.gz 3455629 BLAKE2B 2c1c1adb16826b8048f0a92b35d43b0f308aed2e543d2868f9f497c27f19a9d6da5b6bdd72b3b1f7b30783d1efd0e0c7eb51f6cf44f401b4f8149146944fbb5d SHA512 40220c9fca5bee59b66757162ff2279c2ab221cca07532c64ed3606a95a787080cd4d6bf301ca6d20d8ba4f0c2166e5785fc0ad81ed6528eb527f24d59e79cc8 diff --git a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch deleted file mode 100644 index 5b15108b3bf..00000000000 --- a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch +++ /dev/null @@ -1,21 +0,0 @@ - t_coffee_source/makefile | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile -index 9e01ba0..026b714 100644 ---- a/t_coffee_source/makefile -+++ b/t_coffee_source/makefile -@@ -1,6 +1,6 @@ - - t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -- $(CC) $(CFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm -+ $(CC) $(CFLAGS) $(LDFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm - - all: t_coffee TMalign - -@@ -8,4 +8,4 @@ clean: - rm *.o - - TMalign: -- $(FCC) TMalign.f -o TMalign -+ $(FC) $(FCLAGS) $(LDFLAGS) TMalign.f -o TMalign diff --git a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild deleted file mode 100644 index 919287c790f..00000000000 --- a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic toolchain-funcs - -MY_HASH="8cbe486" -MY_PV="${PV}.${MY_HASH}" -MY_P="T-COFFEE_distribution_Version_${MY_PV}" - -DESCRIPTION="A multiple sequence alignment package" -HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" -SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" - -RDEPEND=" - sci-biology/clustalw - sci-chemistry/tm-align" -DEPEND="" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - sed \ - -e '/@/s:.*;:\t:g' \ - -e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \ - -i t_coffee_source/makefile || die - epatch \ - "${FILESDIR}"/${P}-mayhem.patch \ - "${FILESDIR}"/${P}-set_proper_dir_permissions.patch -} - -src_compile() { - [[ $(gcc-version) == "3.4" ]] || \ - [[ $(gcc-version) == "4.1" ]] && \ - append-flags -fno-unit-at-a-time - emake \ - V=1 \ - CC="$(tc-getCXX)" \ - CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \ - -C t_coffee_source t_coffee -} - -src_install() { - dobin t_coffee_source/t_coffee - - if use examples; then - insinto /usr/share/${PN} - doins -r example - fi -} diff --git a/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild deleted file mode 100644 index 9f32c135fb7..00000000000 --- a/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic fortran-2 toolchain-funcs versionator - -MY_PV="$(replace_version_separator 2 .r)" -MY_P="T-COFFEE_distribution_Version_${MY_PV}" - -DESCRIPTION="A multiple sequence alignment package" -HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" -SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 ppc ~ppc64 x86 ~amd64-linux ~x86-linux" -IUSE="examples" - -RDEPEND=" - sci-biology/clustalw - sci-chemistry/tm-align" -DEPEND="" - -S="${WORKDIR}/${MY_P}" - -die_compile() { - echo - eerror "If you experience an internal compiler error (consult the above" - eerror "messages), try compiling t-coffee using very modest compiler flags." - eerror "See bug #114745 on the Gentoo Bugzilla for more details." - die "Compilation failed" -} - -src_prepare() { - epatch "${FILESDIR}"/${P}-flags.patch -} - -src_compile() { - [[ $(gcc-version) == "3.4" ]] || \ - [[ $(gcc-version) == "4.1" ]] && \ - append-flags -fno-unit-at-a-time - emake \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" \ - -C t_coffee_source t_coffee -} - -src_install() { - dobin t_coffee_source/t_coffee - - if use examples; then - insinto /usr/share/${PN} - doins -r example - fi -}