4 files changed, 0 insertions, 135 deletions
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index fab971d3109c..447e11259498 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 5b15108b3bfa..000000000000
--- 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) $(LDFLAGS) TMalign.f -o TMalign
diff --git a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild
deleted file mode 100644
index 919287c790f8..000000000000
--- a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-MY_HASH="8cbe486"
-MY_PV="${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 9f32c135fb78..000000000000
--- 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
-}