Version bump, included test, respecting LDFLAGS and keyworded for linux prefix

(Portage version: 2.2_rc67/cvs/Linux x86_64)

4 files changed, 109 insertions, 1 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index bfc0d823f4a4..f76a00ca8a26 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/t-coffee
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.40 2010/01/03 14:23:29 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.41 2010/06/15 13:47:35 jlec Exp $
+
+*t-coffee-8.69 (15 Jun 2010)
+
+  15 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/8.69-flags.patch,
+  +t-coffee-8.69.ebuild, +files/8.69-test.patch:
+  Version bump, included test, respecting LDFLAGS and keyworded for linux
+  prefix
 
   03 Jan 2010; Pacho Ramos <pacho@gentoo.org> t-coffee-8.14.ebuild:
   amd64 stable, bug 298765
diff --git a/sci-biology/t-coffee/files/8.69-flags.patch b/sci-biology/t-coffee/files/8.69-flags.patch
new file mode 100644
index 000000000000..0798c2a078b2
--- /dev/null
+++ b/sci-biology/t-coffee/files/8.69-flags.patch
@@ -0,0 +1,18 @@
+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) ${LDFLAGS} TMalign.f -o TMalign
diff --git a/sci-biology/t-coffee/files/8.69-test.patch b/sci-biology/t-coffee/files/8.69-test.patch
new file mode 100644
index 000000000000..3c030566b515
--- /dev/null
+++ b/sci-biology/t-coffee/files/8.69-test.patch
@@ -0,0 +1,11 @@
+diff --git a/bin/test.pl b/bin/test.pl
+index 145be47..81c50bd 100755
+--- a/bin/test.pl
++++ b/bin/test.pl
+@@ -1,5 +1,5 @@
+ #!/usr/bin/env perl
+ chdir "./test";
+-$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
new file mode 100644
index 000000000000..c08ac6cf7813
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-8.69.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2010 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 1.1 2010/06/15 13:47:35 jlec Exp $
+
+EAPI="2"
+
+inherit 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_${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="sci-biology/clustalw"
+DEPEND="${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 || die "Failed to install program."
+
+	insinto /usr/share/${PN}/lib/html
+	doins "${TCDIR}"/html/* \
+		|| die "Failed to install Web interface files."
+
+	cd "${TCDIR}"/doc
+	dodoc aln_compare.doc.txt seq_reformat.doc.txt \
+			t_coffee_technical.txt t_coffee_tutorial.txt \
+			|| die "Failed to install text documentation."
+
+	dohtml t_coffee_technical.htm t_coffee_tutorial.htm \
+		|| die "Failed to install HTML documentation."
+
+	insinto /usr/share/doc/${PF}
+	doins t_coffee_technical.doc t_coffee_tutorial.doc \
+		|| die "Failed to install DOC documentation."
+
+	insinto /usr/share/${PN}
+	doins -r "${TCDIR}"/example \
+		|| die "Failed to install example files."
+}