[gentoo-commits] repo/gentoo:master commit in: sci-biology/t-coffee/, sci-biology/t-coffee/files/
commit: 13297a735a8c0e36ab552d244f4935d21400d310
Author: David Seifert gentoo org>
AuthorDate: Thu Jul 7 19:57:12 2022 +
Commit: David Seifert gentoo org>
CommitDate: Thu Jul 7 19:57:12 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=13297a73
sci-biology/t-coffee: update EAPI 6 -> 8
Signed-off-by: David Seifert gentoo.org>
.../t-coffee/files/t-coffee-11.00-makefile.patch | 19 +++
...ee-11.00-r2.ebuild => t-coffee-11.00-r3.ebuild} | 27 --
2 files changed, 29 insertions(+), 17 deletions(-)
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch
b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch
new file mode 100644
index ..b7a6d9e17a5e
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch
@@ -0,0 +1,19 @@
+--- a/t_coffee_source/makefile
b/t_coffee_source/makefile
+@@ -1,14 +1,12 @@
+-CC=g++
+-CFLAGS=-O3 -Wno-write-strings
+ SOURCES := $(shell find . -type f -name *.c)
+ OBJECTS := $(SOURCES:.c=.o)
+ DEPS := $(OBJECTS:.o=.deps)
+
+ t_coffee: $(OBJECTS)
+- @echo " Linking..."; $(CC) $^ -o t_coffee -lm
++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o t_coffee -lm $(LIBS)
+
+ %.o: %.c
+- @echo " CC $<"; $(CC) $(CFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $<
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $<
+
+ -include $(DEPS)
+
diff --git a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild
b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild
similarity index 66%
rename from sci-biology/t-coffee/t-coffee-11.00-r2.ebuild
rename to sci-biology/t-coffee/t-coffee-11.00-r3.ebuild
index df1859afb208..0064cc319f47 100644
--- a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild
+++ b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
-inherit toolchain-funcs
+inherit flag-o-matic toolchain-funcs
MY_HASH="4466924"
MY_PV="${PV}.${MY_HASH}"
@@ -12,6 +12,7 @@ MY_P="${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;
+S="${WORKDIR}/${MY_P}"
LICENSE="GPL-2"
SLOT="0"
@@ -20,35 +21,27 @@ 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
+ "${FILESDIR}"/${P}-makefile.patch
)
-src_prepare() {
- default
- sed \
- -e '/@/s:.*;:\t:g' \
- -e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \
- -i t_coffee_source/makefile || die
+src_configure() {
+ tc-export CXX
+ append-cxxflags -Wno-write-strings -Wno-unused-result
}
src_compile() {
- emake \
- V=1 \
- CC="$(tc-getCXX)" \
- CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \
- -C t_coffee_source t_coffee
+ emake -C t_coffee_source t_coffee
}
src_install() {
dobin t_coffee_source/t_coffee
- insinto /usr/share/${PN}
+ insinto /usr/share/t-coffee
doins -r example
}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/t-coffee/, sci-biology/t-coffee/files/
commit: f1a2182baa171c729f5c2134144664780e041f37 Author: David Seifert gentoo org> AuthorDate: Mon Dec 25 10:02:15 2017 + Commit: David Seifert gentoo org> CommitDate: Mon Dec 25 16:09:07 2017 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f1a2182b sci-biology/t-coffee: Remove old Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/t-coffee/Manifest | 2 - .../t-coffee/files/t-coffee-9.03.1318-flags.patch | 21 sci-biology/t-coffee/t-coffee-11.00-r1.ebuild | 56 -- sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild | 56 -- 4 files changed, 135 deletions(-) diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest index fab971d3109..447e1125949 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 5b15108b3bf..000 --- 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
[gentoo-commits] repo/gentoo:master commit in: sci-biology/t-coffee/, sci-biology/t-coffee/files/
commit: 6f595002c210652e224701d2483de54e8b195c56
Author: David Seifert gentoo org>
AuthorDate: Sun Dec 24 19:36:03 2017 +
Commit: David Seifert gentoo org>
CommitDate: Sun Dec 24 19:46:08 2017 +
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 000..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 000..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 000..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
