* [gentoo-commits] repo/gentoo:master commit in: sci-biology/t-coffee/, sci-biology/t-coffee/files/
@ 2017-12-24 19:46 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-12-24 19:46 UTC (permalink / raw
To: gentoo-commits
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
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/t-coffee/, sci-biology/t-coffee/files/
@ 2017-12-25 16:09 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-12-25 16:09 UTC (permalink / raw
To: gentoo-commits
commit: f1a2182baa171c729f5c2134144664780e041f37
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Dec 25 10:02:15 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Dec 25 16:09:07 2017 +0000
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..00000000000
--- 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) $(LDFLAGS) TMalign.f -o TMalign
diff --git a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild
deleted file mode 100644
index 919287c790f..00000000000
--- a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-MY_HASH="8cbe486"
-MY_PV="${PV}.${MY_HASH}"
-MY_P="T-COFFEE_distribution_Version_${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}"
-
-src_prepare() {
- 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)" \
- CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \
- -C t_coffee_source t_coffee
-}
-
-src_install() {
- dobin t_coffee_source/t_coffee
-
- if use examples; then
- insinto /usr/share/${PN}
- doins -r example
- fi
-}
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 9f32c135fb7..00000000000
--- 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
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/t-coffee/, sci-biology/t-coffee/files/
@ 2022-07-07 19:58 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2022-07-07 19:58 UTC (permalink / raw
To: gentoo-commits
commit: 13297a735a8c0e36ab552d244f4935d21400d310
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 7 19:57:12 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Jul 7 19:57:12 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=13297a73
sci-biology/t-coffee: update EAPI 6 -> 8
Signed-off-by: David Seifert <soap <AT> 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 000000000000..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
}
^ permalink raw reply related [flat|nested] 3+ messages in thread
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2022-07-07 19:58 [gentoo-commits] repo/gentoo:master commit in: sci-biology/t-coffee/, sci-biology/t-coffee/files/ David Seifert
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2017-12-25 16:09 David Seifert
2017-12-24 19:46 David Seifert
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