commit: 6f595002c210652e224701d2483de54e8b195c56 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Dec 24 19:36:03 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Dec 24 19:46:08 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6f595002
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 sci-biology/t-coffee/Manifest | 1 + .../t-coffee/files/t-coffee-11.00-cxx11.patch | 21 +++++++++ .../t-coffee/files/t-coffee-11.00-gcc7.patch | 22 +++++++++ sci-biology/t-coffee/t-coffee-11.00-r2.ebuild | 54 ++++++++++++++++++++++ 4 files changed, 98 insertions(+) diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest index dd94e03190c..fab971d3109 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 00000000000..17817d30eca --- /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 00000000000..64afc04a4b5 --- /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 00000000000..df1859afb20 --- /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 +}
