gentoo resync : 25.12.2017

6 files changed, 62 insertions, 99 deletions

diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index 7101d6d36441..a37eb2942b96 100644
--- a/sci-biology/t-coffee/Manifest
+++ b/sci-biology/t-coffee/Manifest
@@ -1,8 +1,7 @@
+AUX t-coffee-11.00-cxx11.patch 988 BLAKE2B 03caf7bf7a10b22f8dc7e98f672564d4346123f04f8505f4fca040c10cb36031b8891dbe3f661b18f61520ebf48e2c8cc2a53d11b21c44d7d6c06728950e3eba SHA512 d97320c97467b64399ffe5917cbae4e7bac37c57f66eedbaad889f5db60b1da0d57bb4ced716dd97e907f4569789183175e531b10e7577560e18050584dd1598
+AUX t-coffee-11.00-gcc7.patch 864 BLAKE2B a5f18fc86764d69cf584e976e88e4ce08f5299bfa4410ebff5ebf97dd29e8d4995076d921517d05138dbc37525d2e5f370194c0f6962cd4e2ff43bdee7c3f7c1 SHA512 d96c61f5efb1e89750a2fbb2369fdb6d831ad7c093eb2b4237af1ff21528990578399ecc1bb0f1668086084427902922003407eb1bb19f43fa25c0bcc01789a6
 AUX t-coffee-11.00-mayhem.patch 1230 BLAKE2B cd54632fb5760f9d76d9e72d69c2d893e0812277c6de7414546a699cf8d98b497273f9ce3f61407181d6c7f0ea0d7720b1de10c02304b92a7d76db3e2732b023 SHA512 b2c232f3e517c9c944c3d13a96b8383f8875e2e968ed16df25e37c6bfeee106cf82f9107187081753fbcaba6e27713fe5f4ca51d2f859ea7e8744f3b2b41f035
 AUX t-coffee-11.00-set_proper_dir_permissions.patch 1203 BLAKE2B 220f1932cfab4f3d39cfcf3191754c2a2705c75c9cce8f11d04fb3fe8e3c3e60a10251b01c2109faad2fda4a5ce57ee5e5e598a0ec841c3bb0fa19d0e8e4d636 SHA512 fb19aae00ccc0824bcb757d32ee921159e9ece9c0336b3d663e0140ccfca77bf3fcce0eeb304517e41dc1dd4c9469c345c0c35fe8e7fdf120c6fddba4a4e1524
-AUX t-coffee-9.03.1318-flags.patch 3376 BLAKE2B c578abe18e4ea8b038789c55887c1f1973ff62dc5a9ae28c6b7a959e221d818909bd98b29492b56d64a81c7c408a259b979b4e73f7ef948b605787a61dd2f61e SHA512 db1d4463280a95ce644065c64a653d31d57d144c45afba5ff1dd03911ce3c3c1afb15a29c09b4089558acc364385e3eeddbf9179c662191d730d34e09675243c
-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
-EBUILD t-coffee-11.00-r1.ebuild 1279 BLAKE2B 884bd4f7397dd7a8f170299d515e137f7773c58046011879b4d98d7da86199a4541c29cbad685221fbf668c02e683461f230922ead73d7beade10dc01a656c42 SHA512 e2e5c6027efc490de8f83bcfdd32fa67ad1b1e40539ccf3e8e2523a7242cdd24621877afaa5f6ed8998e68919faaa439ae8a010638c60c2123b6423cec2a1a3b
-EBUILD t-coffee-9.03.1318-r1.ebuild 1335 BLAKE2B 2c4c5aaf24cd09f76643a7d87d942ae2cb699e6f427515454ef2af8e0b6cecc4a1797034b054db4dd2fbf38595274950d02e05d431c75464d4f985e72e229f74 SHA512 92e0607a498f4d84b297d492bf3e12b6565e25ded94e77e6703ea3b5d9745fb1c6cd7d4f8914fd859cf4ccea8c595069669dd47a607901054a344f6c564ab8a2
+DIST T-COFFEE_distribution_Version_11.00.4466924.tar.gz 3502302 BLAKE2B 0d8087eb219ff72e6f478a779ccdb51e7aee861236c522dec5391e854b0b0bf6eab324009686237e6d334d2e13e17700f6692333060a2ed55711380ef2ab2cdb SHA512 c6c1a7b768156f8457dc4c53a77b14ce0b85e591d60762faf6e6f6f3b60dab75e99449d55b42ef3af1c90e244f735e19abb72d0ce871bb9fbfbb8d1641531293
+EBUILD t-coffee-11.00-r2.ebuild 1163 BLAKE2B 7b7dd0de076fa4bb9ac5b59d55df39a118b19f333851beccceeb511f3a780f5bfc2128b29cabd0304320810ea373ed15971eb061604da87d8aeae427876d9167 SHA512 7701957be90259bc4cac73bd3a280d5181432a1d6d30c4223fa4b1c6e497b50ec60b605a5a609068d9139bc3bf3183cf1d1860ece76542952dd3a289996d2b87
 MISC metadata.xml 762 BLAKE2B 38e430b2aa0736102b7c8b958c3854723f0d5c88a9301240f9a20d8cdd6f24628ba735aea82d7a379b93d93dc3845e963e9624045933886a2bc09658eaf7827c SHA512 fe31bf756f5e3dbb048e691ecd01ee86000f65ae4f5c19df3c5c3e2deb7fb8ffa83ed39c317188302a8cf2a0d152323a0258497cfb0e3e355dded08b060d0310
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch b/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch
new file mode 100644
index 000000000000..17817d30eca2
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-cxx11.patch
@@ -0,0 +1,21 @@
+--- a/t_coffee_source/programmes_define.h
++++ b/t_coffee_source/programmes_define.h
+@@ -390,12 +390,12 @@
+ #define XMLSIMPLE_language2 "Perl"
+ #define XMLSIMPLE_source "empty"
+ #define XMLSIMPLE_mode "psicoffee,expresso,accurate"
+-#define x3dna-ssr_4_TCOFFEE "x3dna"
+-#define x3dna-ssr_type "RNA_secondarystructure_predictor"
+-#define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/"
+-#define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz"
+-#define x3dna-ssr_mode "saracoffee"
+-#define x3dna-ssr_update_action "never"
++#define x3dna_ssr_4_TCOFFEE "x3dna"
++#define x3dna_ssr_type "RNA_secondarystructure_predictor"
++#define x3dna_ssr_ADDRESS "http://x3dna.bio.columbia.edu/"
++#define x3dna_ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz"
++#define x3dna_ssr_mode "saracoffee"
++#define x3dna_ssr_update_action "never"
+ //TclinkdbEnd
+ /*New Methods*/
+ /********************************************/
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch b/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch
new file mode 100644
index 000000000000..64afc04a4b50
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-gcc7.patch
@@ -0,0 +1,22 @@
+--- a/t_coffee_source/util_lib/aln_convertion_util.c
++++ b/t_coffee_source/util_lib/aln_convertion_util.c
+@@ -5592,7 +5592,7 @@
+ 
+ 	     list=string2list (H->seq_comment[n]);
+ 	     if ( list==NULL || atoi(list[0])==1)continue;
+-	     S->seq_comment[a]='\0';
++	     S->seq_comment[a]=NULL;
+ 	     sprintf (S->name[a], "%s%s%s",H->name[n], list[1], list[2]);
+ 	     vfree ( S->seq_comment[a]);S->seq_comment[a]=(char*)vcalloc ( strlen (H->seq_comment[n])+1, sizeof (char));
+ 	     for (b=3; b< atoi(list[0]); b++)S->seq_comment[a]=strcat (S->seq_comment[a], list[b]);
+--- a/t_coffee_source/util_lib/util.c
++++ b/t_coffee_source/util_lib/util.c
+@@ -5946,7 +5946,7 @@
+ 		  val_array[a]=(char*)vrealloc (val_array[a], strlen (v)+1);
+ 		  sprintf (val_array[a],"%s",v);
+ 		}
+-	      else val_array[a]='\0';
++	      else val_array[a]=NULL;
+ 	      return v;
+ 	    }
+ 	}
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-r2.ebuild
index 919287c790f8..df1859afb208 100644
--- a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild
+++ b/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild
@@ -1,22 +1,21 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=6
 
-inherit eutils flag-o-matic toolchain-funcs
+inherit toolchain-funcs
 
-MY_HASH="8cbe486"
+MY_HASH="4466924"
 MY_PV="${PV}.${MY_HASH}"
-MY_P="T-COFFEE_distribution_Version_${MY_PV}"
+MY_P="${PN^^}_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"
+SRC_URI="http://www.tcoffee.org/Packages/Beta/Latest/${MY_P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
 
 RDEPEND="
 	sci-biology/clustalw
@@ -24,21 +23,22 @@ RDEPEND="
 DEPEND=""
 
 S="${WORKDIR}/${MY_P}"
+PATCHES=(
+	"${FILESDIR}"/${P}-mayhem.patch
+	"${FILESDIR}"/${P}-set_proper_dir_permissions.patch
+	"${FILESDIR}"/${P}-cxx11.patch
+	"${FILESDIR}"/${P}-gcc7.patch
+)
 
 src_prepare() {
+	default
 	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)" \
@@ -49,8 +49,6 @@ src_compile() {
 src_install() {
 	dobin t_coffee_source/t_coffee
 
-	if use examples; then
-		insinto /usr/share/${PN}
-		doins -r example
-	fi
+	insinto /usr/share/${PN}
+	doins -r example
 }
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
-}