sci-biology/t-coffee: Fix building with GCC 7

Closes: https://bugs.gentoo.org/639832
Package-Manager: Portage-2.3.19, Repoman-2.3.6

4 files changed, 98 insertions, 0 deletions

diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index dd94e03190cb..fab971d3109c 100644
--- a/sci-biology/t-coffee/Manifest
+++ b/sci-biology/t-coffee/Manifest
@@ -1,2 +1,3 @@
+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-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/t-coffee-11.00-r2.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild
new file mode 100644
index 000000000000..df1859afb208
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+MY_HASH="4466924"
+MY_PV="${PV}.${MY_HASH}"
+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/Beta/Latest/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+	sci-biology/clustalw
+	sci-chemistry/tm-align"
+DEPEND=""
+
+S="${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) $(LDFLAGS):g' \
+		-i t_coffee_source/makefile || die
+}
+
+src_compile() {
+	emake \
+		V=1 \
+		CC="$(tc-getCXX)" \
+		CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \
+		-C t_coffee_source t_coffee
+}
+
+src_install() {
+	dobin t_coffee_source/t_coffee
+
+	insinto /usr/share/${PN}
+	doins -r example
+}