Drop old

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 23 insertions, 107 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index 5b7e0bb9e3b1..72716245f206 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/t-coffee
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.57 2015/04/26 16:59:53 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.58 2015/05/05 13:40:54 jlec Exp $
+
+  05 May 2015; Justin Lecher <jlec@gentoo.org> -files/8.69-flags.patch,
+  -files/8.69-test.patch, -t-coffee-8.69.ebuild:
+  Drop old
 
   26 Apr 2015; Pacho Ramos <pacho@gentoo.org> t-coffee-9.03.1318-r1.ebuild:
   ppc stable wrt bug #544930
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index 455f561442ab..d7890223c2ff 100644
--- a/sci-biology/t-coffee/Manifest
+++ b/sci-biology/t-coffee/Manifest
@@ -1,21 +1,29 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
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-AUX 8.69-test.patch 524 SHA256 05ad8d6a9bce520d49ed7de18143067858346b18766f42e597cc0974d4d8957a SHA512 60fdce6c19f04f13d330561546af4b8569cfaefd2dfb9d43205e4db400eb352f62d3ae247128585bb0aa757a8d880738865b8b5b3dfbce0a639397eb278e1b0f WHIRLPOOL 91ca49c48571431240ecd1b44fb6d7b37f6b25aa2b80240f8daac6e822278ae241fa8875df3240b598fb1475ffebf6226986a2254b0fdf69ef0f0944959ae62c
 AUX t-coffee-9.03.1318-flags.patch 3376 SHA256 a6519f65d456bd62860444960f2978de884a1a9a83c4558904277629cbfc8b32 SHA512 db1d4463280a95ce644065c64a653d31d57d144c45afba5ff1dd03911ce3c3c1afb15a29c09b4089558acc364385e3eeddbf9179c662191d730d34e09675243c WHIRLPOOL 3f362b8437f1351b6f33eb25761189c783312e397228bbd70a58ff188ded2c5abbed980fb23231cbce240272872edcbc24d3b5556934f148dbeb6f1c74fee1d8
 DIST T-COFFEE_distribution_Version_11.00.8cbe486.tar.gz 3526354 SHA256 b8018433574ff7705c49cd974bebb06a48eb8bc5e38aaa9eb4f53f2e7778e72c SHA512 5c486411bae430cfca6f4623f4dff348e2d9ab7c2eb0edef8059c6cb9c01ee48347e06be0c5d19ee1ace4b9f597f19beee8da2d7eecba29c5a78c2aec800be92 WHIRLPOOL 205eb1b416b38c4d86722ec501d815cc3f9f974a79e07f6fff32855972a9d3a9849585ca345fa66bbcbe15dca8f16930e7bafe44ce5d39e23f9f73023da13b7c
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 EBUILD t-coffee-11.00.ebuild 1294 SHA256 0ba548d632fec4e1a745d1501c79ec9d4f840747ac6c87a9f9cc5c0bbcd8a6a2 SHA512 f308a0e94c9043b16396cb8aeee28ebc1c4af6daf008108e0a9a2f71f00ca4ce1c8b5c5b93bbfe41287b67937193a3ae7f7c09fe628d437f9f93a14a4e5c6f9a WHIRLPOOL 84e923f86609acdd71e046c8b7e9f25c5dcdee792b0db41e0f4afc7186d322700bbd092a5cfe301b4bf23c94012006c8620724f5641fd60ecc43a745c34b9612
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 MISC metadata.xml 668 SHA256 39cab5771c827201b3b0569126729f00bd02202bd3e39b02e788ad96353f292b SHA512 b256c17f22d2a1d7c0cf5095e342c5b2d44165dac85daab618784f47f3f334bec0e213f18ac6765e65844339216231aa361dd9a75db663a57c736c05e13a6cbf WHIRLPOOL 338a3049344c24d204eba386220e8c5b0f313e8275230a67b072c005fc30bd91abce213fa5e01e920bc750ff92ffe0cb414b0e7ac363efb2b48c934554cffea6
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diff --git a/sci-biology/t-coffee/files/8.69-flags.patch b/sci-biology/t-coffee/files/8.69-flags.patch
deleted file mode 100644
index 0798c2a078b2..000000000000
--- a/sci-biology/t-coffee/files/8.69-flags.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile
-index d2d00da..2357c44 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 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 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 t_coffee.o  -lm
- 
- all:  t_coffee TMalign
- 
-@@ -8,4 +8,4 @@ clean:
- 	rm *.o
- 
- TMalign:
--	 $(FCC) TMalign.f -o TMalign
-+	 $(FCC) $(FFLAGS) ${LDFLAGS} TMalign.f -o TMalign
diff --git a/sci-biology/t-coffee/files/8.69-test.patch b/sci-biology/t-coffee/files/8.69-test.patch
deleted file mode 100644
index 3c030566b515..000000000000
--- a/sci-biology/t-coffee/files/8.69-test.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff --git a/bin/test.pl b/bin/test.pl
-index 145be47..81c50bd 100755
---- a/bin/test.pl
-+++ b/bin/test.pl
-@@ -1,5 +1,5 @@
- #!/usr/bin/env perl
- chdir "./test";
--$r=system "../bin/t_coffee test.pep -method fast_pair -outfile=new_reference_test.aln -outorder=input>/dev/null";
-+$r=system "../t_coffee_source/t_coffee test.pep -method fast_pair -outfile=new_reference_test.aln -outorder=input>/dev/null";
- if ($r==0){print "\nInstallation of t_coffee Successful\n";}
- else {print "\nInstallation of t_coffee Not Successful\n";}
diff --git a/sci-biology/t-coffee/t-coffee-8.69.ebuild b/sci-biology/t-coffee/t-coffee-8.69.ebuild
deleted file mode 100644
index 645f1f61c172..000000000000
--- a/sci-biology/t-coffee/t-coffee-8.69.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-8.69.ebuild,v 1.7 2015/02/09 12:50:38 blueness Exp $
-
-EAPI="2"
-
-inherit eutils flag-o-matic toolchain-funcs
-
-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/T-COFFEE_distribution_Version_${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE="examples test"
-KEYWORDS="amd64 ppc ~ppc64 x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="sci-biology/clustalw"
-DEPEND="${DEPEND}
-	test? ( dev-lang/perl )"
-
-S="${WORKDIR}/T-COFFEE_distribution_Version_${PV}"
-
-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 "${FILESDIR}"/${PV}-flags.patch
-	epatch "${FILESDIR}"/${PV}-test.patch
-}
-
-src_compile() {
-	[[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time
-	[[ $(gcc-version) == "4.1" ]] && append-flags -fno-unit-at-a-time
-	emake \
-		CC="$(tc-getCC)" CFLAGS="${CFLAGS}" \
-		-C t_coffee_source || die_compile
-}
-
-src_test() {
-	cd "${TCDIR}"
-	perl bin/test.pl || die
-}
-
-src_install() {
-	dobin t_coffee_source/t_coffee || die "Failed to install program."
-
-	insinto /usr/share/${PN}/lib/html
-	doins html/* || die "Failed to install Web interface files."
-
-#	cd IR}"/doc
-	dodoc doc/*.txt || die "Failed to install text documentation."
-	dohtml doc/*.htm || die "Failed to install HTML documentation."
-
-	insinto /usr/share/doc/${PF}
-	doins doc/*.doc || die "Failed to install DOC documentation."
-
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r example || die "Failed to install example files."
-	fi
-}