[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/, sci-biology/allpathslg/files/
commit: 59414166be981c4e44e9c712fd4474b428eb482d
Author: Mikle Kolyada gentoo org>
AuthorDate: Mon Jul 22 10:05:08 2019 +
Commit: Mikle Kolyada gentoo org>
CommitDate: Mon Jul 22 10:05:08 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59414166
sci-biology/allpathslg: remove last rited package
Signed-off-by: Mikle Kolyada gentoo.org>
sci-biology/allpathslg/Manifest| 2 -
sci-biology/allpathslg/allpathslg-52488-r2.ebuild | 46 --
.../allpathslg/files/allpathslg-52488-gcc7.patch | 13 --
sci-biology/allpathslg/metadata.xml| 8
4 files changed, 69 deletions(-)
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
deleted file mode 100644
index 22364d00b07..000
--- a/sci-biology/allpathslg/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST allpathslg-52488-patchset.tar.bz2 11405 BLAKE2B
7a4c36884ac95a4eb23291720e422ce1ec41d0bea3a0b10582aa1d8154234971eb8d06979a969e65c1ec1eab031d2500a1ec40809019c8b4aa1d1d2e81427dbe
SHA512
a1d58c131afeef04a9d7a2520fcd28a853317323fdcab1a253cb2548546bbc559993c74a68a8032a5d0e865ac2c2d53ff6b4c149aade2d1f87a2ab4116ebe4cc
-DIST allpathslg-52488.tar.gz 3121949 BLAKE2B
b75904f9e8256a14c97abae45a0cb41718f95d27a4a072b6144bd125abb57682faa180de6a18399ab4fa43988344c436ca1eab8412433353fcc746c432c33031
SHA512
c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d
diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
deleted file mode 100644
index cc9498b65f7..000
--- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools flag-o-matic toolchain-funcs
-
-DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
-# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd;
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz
- https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- !sci-biology/allpaths
- !sci-biology/vaal"
-DEPEND="
- ${RDEPEND}
- dev-libs/boost:="
-
-PATCHES=(
- "${WORKDIR}"/${P}-patchset/${P}_fix-buildsystem.patch
- "${WORKDIR}"/${P}-patchset/${P}_remove-namespace-std.patch
- "${FILESDIR}"/${P}-gcc7.patch
-)
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-src_prepare() {
- default
-
- # Fix building with glibc-2.27, bug #647340
- sed -i -e 's/-mieee-fp//' configure.ac || die
-
- eautoreconf
-}
diff --git a/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch
b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch
deleted file mode 100644
index 7c5e1267e4e..000
--- a/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch
+++ /dev/null
@@ -1,13 +0,0 @@
a/src/paths/long/VariantCallTools.cc
-+++ b/src/paths/long/VariantCallTools.cc
-@@ -1870,8 +1870,8 @@
- bool i_is_indel = (change[i].first.size() != change[i].second.size());
- if (i_is_indel) inserted_base += change[i].second.size()-1;
- size_t j = i + 1;
--while (j < edits.size() && abs(edits[j].second - edits[j-1].second
--- change[j-1].first.size()) < MinClumpSep) {
-+while (j < edits.size() && std::abs(edits[j].second -
edits[j-1].second
-+- static_cast(change[j-1].first.size())) <
MinClumpSep) {
- nmatch += edits[j].second - edits[j-1].second -
change[j-1].first.size();
- bool j_is_indel = (change[j].first.size() !=
change[j].second.size());
- if (j_is_indel)
diff --git a/sci-biology/allpathslg/metadata.xml
b/sci-biology/allpathslg/metadata.xml
deleted file mode 100644
index 959160fe46b..000
--- a/sci-biology/allpathslg/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
-sci-biol...@gentoo.org
-Gentoo Biology Project
-
-
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/
commit: edca5a71f730e3c24b0704faeccb1b879c23e2be
Author: Pacho Ramos gentoo org>
AuthorDate: Sun Oct 21 15:05:09 2018 +
Commit: Pacho Ramos gentoo org>
CommitDate: Sun Oct 21 15:17:26 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=edca5a71
sci-biology/allpathslg: Fix build with glibc-2.27
Closes: https://bugs.gentoo.org/647340
Signed-off-by: Pacho Ramos gentoo.org>
Package-Manager: Portage-2.3.51, Repoman-2.3.11
sci-biology/allpathslg/allpathslg-52488-r2.ebuild | 5 -
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
index 964904d6655..cc9498b65f7 100644
--- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -39,5 +39,8 @@ pkg_setup() {
src_prepare() {
default
+ # Fix building with glibc-2.27, bug #647340
+ sed -i -e 's/-mieee-fp//' configure.ac || die
+
eautoreconf
}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/files/, sci-biology/allpathslg/
commit: cd124fce591dc879a82805175313c4b2e0ef18a6
Author: David Seifert gentoo org>
AuthorDate: Sun Dec 24 17:11:30 2017 +
Commit: David Seifert gentoo org>
CommitDate: Sun Dec 24 18:00:22 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cd124fce
sci-biology/allpathslg: Fix building with GCC 7
Closes: https://bugs.gentoo.org/638724
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/allpathslg/allpathslg-52488-r2.ebuild| 5 +++--
sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch | 13 +
2 files changed, 16 insertions(+), 2 deletions(-)
diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
index e68430e2462..391575f4f05 100644
--- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
@@ -23,8 +23,9 @@ DEPEND="
dev-libs/boost:="
PATCHES=(
- "${WORKDIR}/${P}-patchset/${P}_fix-buildsystem.patch"
- "${WORKDIR}/${P}-patchset/${P}_remove-namespace-std.patch"
+ "${WORKDIR}"/${P}-patchset/${P}_fix-buildsystem.patch
+ "${WORKDIR}"/${P}-patchset/${P}_remove-namespace-std.patch
+ "${FILESDIR}"/${P}-gcc7.patch
)
pkg_pretend() {
diff --git a/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch
b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch
new file mode 100644
index 000..7c5e1267e4e
--- /dev/null
+++ b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch
@@ -0,0 +1,13 @@
+--- a/src/paths/long/VariantCallTools.cc
b/src/paths/long/VariantCallTools.cc
+@@ -1870,8 +1870,8 @@
+ bool i_is_indel = (change[i].first.size() != change[i].second.size());
+ if (i_is_indel) inserted_base += change[i].second.size()-1;
+ size_t j = i + 1;
+-while (j < edits.size() && abs(edits[j].second - edits[j-1].second
+-- change[j-1].first.size()) < MinClumpSep) {
++while (j < edits.size() && std::abs(edits[j].second -
edits[j-1].second
++- static_cast(change[j-1].first.size())) <
MinClumpSep) {
+ nmatch += edits[j].second - edits[j-1].second -
change[j-1].first.size();
+ bool j_is_indel = (change[j].first.size() !=
change[j].second.size());
+ if (j_is_indel)
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/
commit: ad80f329e6e91c1c6549c8df3c298a4d1d8a6657
Author: David Seifert gentoo org>
AuthorDate: Sun Dec 24 17:59:40 2017 +
Commit: David Seifert gentoo org>
CommitDate: Sun Dec 24 18:00:27 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ad80f329
sci-biology/allpathslg: Sanitize ebuild
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/allpathslg/allpathslg-52488-r2.ebuild | 19 ++-
1 file changed, 2 insertions(+), 17 deletions(-)
diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
index 391575f4f05..964904d6655 100644
--- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
@@ -29,26 +29,11 @@ PATCHES=(
)
pkg_pretend() {
- # as of release 44849, GCC 4.7.0 (or higher) is required
- # seems pre gcc-4.7 users must stay with:
- #
ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
- if [[ ${MERGE_TYPE} != binary ]]; then
- tc-is-gcc && [[ $(gcc-version) < 4.7 ]] && \
- die "You need to use gcc >4.7"
- fi
+ [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
}
pkg_setup() {
- if ! tc-has-openmp; then
- ewarn "OpenMP is not available in your current selected
compiler"
-
- if tc-is-clang; then
- ewarn "OpenMP support in sys-devel/clang is provided by
sys-libs/libomp,"
- ewarn "which you will need to build ${CATEGORY}/${PN}
with USE=\"openmp\""
- fi
-
- die "need openmp capable compiler"
- fi
+ [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
}
src_prepare() {
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/, sci-biology/allpathslg/files/
commit: b2afaced4f1f7c81e59293698518d9b4f6f8b414
Author: Michał Górny gentoo org>
AuthorDate: Sat Dec 9 23:12:24 2017 +
Commit: Michał Górny gentoo org>
CommitDate: Sat Dec 9 23:13:08 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b2afaced
sci-biology/allpathslg: [QA] Move patches to a distfile
Closes: https://bugs.gentoo.org/620610
sci-biology/allpathslg/Manifest|3 +-
sci-biology/allpathslg/allpathslg-52488-r2.ebuild |9 +-
.../files/allpathslg-52488_fix-buildsystem.patch | 33 -
.../allpathslg-52488_remove-namespace-std.patch| 1770
4 files changed, 7 insertions(+), 1808 deletions(-)
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
index c87071a8893..22364d00b07 100644
--- a/sci-biology/allpathslg/Manifest
+++ b/sci-biology/allpathslg/Manifest
@@ -1 +1,2 @@
-DIST allpathslg-52488.tar.gz 3121949 SHA256
035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542 SHA512
c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d
WHIRLPOOL
c63a13450c55fce8f2c5399bdd5d8f32939e31d9d13a120835b1d826ae96e251fea81caa134d5d45ad857af0777c22e4ad1d894c81a74db6d83a7d9ad83b12b4
+DIST allpathslg-52488-patchset.tar.bz2 11405 BLAKE2B
7a4c36884ac95a4eb23291720e422ce1ec41d0bea3a0b10582aa1d8154234971eb8d06979a969e65c1ec1eab031d2500a1ec40809019c8b4aa1d1d2e81427dbe
SHA512
a1d58c131afeef04a9d7a2520fcd28a853317323fdcab1a253cb2548546bbc559993c74a68a8032a5d0e865ac2c2d53ff6b4c149aade2d1f87a2ab4116ebe4cc
+DIST allpathslg-52488.tar.gz 3121949 BLAKE2B
b75904f9e8256a14c97abae45a0cb41718f95d27a4a072b6144bd125abb57682faa180de6a18399ab4fa43988344c436ca1eab8412433353fcc746c432c33031
SHA512
c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d
diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
index e4c4d95288f..e68430e2462 100644
--- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -8,7 +8,8 @@ inherit autotools flag-o-matic toolchain-funcs
DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd;
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz;
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz
+ https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2;
LICENSE="MIT"
SLOT="0"
@@ -22,8 +23,8 @@ DEPEND="
dev-libs/boost:="
PATCHES=(
- "${FILESDIR}/${P}_fix-buildsystem.patch"
- "${FILESDIR}/${P}_remove-namespace-std.patch"
+ "${WORKDIR}/${P}-patchset/${P}_fix-buildsystem.patch"
+ "${WORKDIR}/${P}-patchset/${P}_remove-namespace-std.patch"
)
pkg_pretend() {
diff --git
a/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch
b/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch
deleted file mode 100644
index 7944eb5469d..000
--- a/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-Fix build system to remove hardcoded debugging flags.
-
allpathslg-52488/configure.ac
-+++ allpathslg-52488/configure.ac
-@@ -12,7 +12,7 @@
- AC_OPENMP
- AC_OPENMP_CHECK
-
--CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo
-Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long
-Wno-parentheses -Wno-unused-parameter -fno-nonansi-builtins -mieee-fp
-fno-strict-aliasing -iquote . -ggdb -DNDEBUG"
-+CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo
-Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long
-Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote .
-DNDEBUG"
-
- OS_RELEASE="`uname -r`"
- AC_SUBST(CXXFLAGS)
allpathslg-52488/m4/broad.m4
-+++ allpathslg-52488/m4/broad.m4
-@@ -35,12 +35,14 @@
- OLD_CFLAGS=$CFLAGS
- CFLAGS="$OPENMP_CFLAGS $CFLAGS"
- AC_MSG_CHECKING([validity of OpenMP configuation.])
--AC_LINK_IFELSE([#ifndef _OPENMP
-+ AC_LINK_IFELSE([
-+AC_LANG_SOURCE([[
-+ #ifndef _OPENMP
- choke me
- #endif
- #include
--int main () { return omp_get_num_threads (); }],
--[],
-+int main () { return omp_get_num_threads (); }
-+]])],[],
- [AC_MSG_BROAD_FAIL([Your compiler must support OpenMP.])])
- CXXFLAGS=$OLD_CXXFLAGS
- CFLAGS=$OLD_CFLAGS
diff --git
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/
commit: f9fe558786e5afc92cfe86f3a0060e64f2acdeeb
Author: David Seifert gentoo org>
AuthorDate: Mon Feb 20 22:07:05 2017 +
Commit: David Seifert gentoo org>
CommitDate: Mon Feb 20 22:10:02 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f9fe5587
sci-biology/allpathslg: Remove old
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/allpathslg/Manifest| 1 -
sci-biology/allpathslg/allpathslg-42337.ebuild | 35 --
2 files changed, 36 deletions(-)
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
index cd18242ec5..c87071a889 100644
--- a/sci-biology/allpathslg/Manifest
+++ b/sci-biology/allpathslg/Manifest
@@ -1,2 +1 @@
-DIST allpathslg-42337.tar.gz 2739498 SHA256
a2c8f64f6ba1705b2331ca07761d189183c6745f8717ffc67ee98e9e3ca3dba6 SHA512
7595fbe14a5029578b57d16f781cbb2a0f0ad6b1af2dd770e2274f8fe2e11d0013fdff12cc85c1be748e769ffb23b7d5fe30920feef38e0e8b947d05b8bda31c
WHIRLPOOL
79bda55d49877641eb55630950472a06d8f25db467dbfecde8b4d04c3ce16c071d32dd312fa9a0f72723bf4caa8f9b1d0346acf438b9671b4bed2c0672c788b9
DIST allpathslg-52488.tar.gz 3121949 SHA256
035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542 SHA512
c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d
WHIRLPOOL
c63a13450c55fce8f2c5399bdd5d8f32939e31d9d13a120835b1d826ae96e251fea81caa134d5d45ad857af0777c22e4ad1d894c81a74db6d83a7d9ad83b12b4
diff --git a/sci-biology/allpathslg/allpathslg-42337.ebuild
b/sci-biology/allpathslg/allpathslg-42337.ebuild
deleted file mode 100644
index 9fb44dfcc9..00
--- a/sci-biology/allpathslg/allpathslg-42337.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit autotools flag-o-matic
-
-DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd;
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz;
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 -x86"
-
-DEPEND="
- dev-libs/boost
- !sci-biology/allpaths
- sci-biology/vaal"
-RDEPEND=""
-
-src_prepare() {
- sed -i 's/-ggdb3//' configure.ac || die
- eautoreconf
-}
-
-src_install() {
- einstall || die
- # Provided by sci-biology/vaal
- for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb
ShortQueryLookup; do
- rm "${D}/usr/bin/$i" || die
- done
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/
commit: aee8fa1dbbe56f8f592e3d4dfc4bc6832126a45a
Author: David Seifert gentoo org>
AuthorDate: Sat Aug 13 10:33:50 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sat Aug 13 10:34:09 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=aee8fa1d
sci-biology/allpathslg: Unconditionally require OpenMP support
Gentoo-bug: 591166
* The configure script of sci-biology/allpathslg allows for
specifying --enable/--disable-openmp, without it actually
being optional.
Package-Manager: portage-2.3.0
...-52488-r1.ebuild => allpathslg-52488-r2.ebuild} | 27 ++
1 file changed, 17 insertions(+), 10 deletions(-)
diff --git a/sci-biology/allpathslg/allpathslg-52488-r1.ebuild
b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
similarity index 67%
rename from sci-biology/allpathslg/allpathslg-52488-r1.ebuild
rename to sci-biology/allpathslg/allpathslg-52488-r2.ebuild
index 268d759..4164bce 100644
--- a/sci-biology/allpathslg/allpathslg-52488-r1.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild
@@ -4,7 +4,7 @@
EAPI=6
-inherit autotools flag-o-matic
+inherit autotools flag-o-matic toolchain-funcs
DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
@@ -14,14 +14,13 @@
SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="openmp"
RDEPEND="
!sci-biology/allpaths
!sci-biology/vaal"
DEPEND="
${RDEPEND}
- dev-libs/boost"
+ dev-libs/boost:="
PATCHES=(
"${FILESDIR}/${P}_fix-buildsystem.patch"
@@ -33,8 +32,21 @@ pkg_pretend() {
# seems pre gcc-4.7 users must stay with:
#
ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
if [[ ${MERGE_TYPE} != binary ]]; then
- [[ $(tc-getCC) == *gcc* ]] && [[ $(gcc-version) < 4.7 ]] && \
- die "You need to use gcc >4.7"
+ tc-is-gcc && [[ $(gcc-version) < 4.7 ]] && \
+ die "You need to use gcc >4.7"
+ fi
+}
+
+pkg_setup() {
+ if ! tc-has-openmp; then
+ ewarn "OpenMP is not available in your current selected
compiler"
+
+ if tc-is-clang; then
+ ewarn "OpenMP support in sys-devel/clang is provided by
sys-libs/libomp,"
+ ewarn "which you will need to build ${CATEGORY}/${PN}
with USE=\"openmp\""
+ fi
+
+ die "need openmp capable compiler"
fi
}
@@ -43,8 +55,3 @@ src_prepare() {
eautoreconf
}
-
-src_configure() {
- econf \
- $(use_enable openmp)
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/files/
commit: 71fb540e91fd211248ed97daee867d9bfe77fa4d
Author: David Seifert gentoo org>
AuthorDate: Thu May 5 18:11:32 2016 +
Commit: David Seifert gentoo org>
CommitDate: Thu May 5 18:11:49 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=71fb540e
sci-biology/allpathslg: replace isnan macro with proper std::isnan function
Gentoo-Bug: 580086
Package-Manager: portage-2.2.28
.../allpathslg-52488_remove-namespace-std.patch| 22 +-
1 file changed, 21 insertions(+), 1 deletion(-)
diff --git
a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch
b/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch
index a094c53..56d0406 100644
--- a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch
+++ b/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch
@@ -890,10 +890,12 @@ https://bugs.gentoo.org/show_bug.cgi?id=568440
bool IsBubbleEdge(int eid, const HyperBasevector& hb, const vec& to_left,
--- allpathslg-52488/src/paths/long/VariantReadSupport.cc
+++ allpathslg-52488/src/paths/long/VariantReadSupport.cc
-@@ -23,6 +23,11 @@
+@@ -23,6 +23,13 @@
#include "paths/long/ReadOriginTracker.h"
#include "paths/long/EvalByReads.h"
++#include
++
+using std::get;
+using std::make_tuple;
+using std::ignore;
@@ -902,6 +904,24 @@ https://bugs.gentoo.org/show_bug.cgi?id=568440
namespace {
void CalcLengthProbSimple(vec,const double dProbIns_len, const
double dProbDel_len, const uint64_t org_length){
const double dProbIns=dProbIns_len;
+@@ -158,7 +165,7 @@
+ for(uint64_t ff=1;ff(n_q_len[ff]) ; ++ll){ dFactor /=
(long double)(ll); }
+ }
+-if( dFactor==std::numeric_limits::infinity() ||
isnan(dFactor) ){ dFactor=1.0; }
++if( dFactor==std::numeric_limits::infinity() ||
std::isnan(dFactor) ){ dFactor=1.0; }
+ if(verbosity>0) std::cout << "dFactor " << dFactor << std::endl;
+
+ long double dDenom=0.0;
+@@ -193,7 +200,7 @@
+ }
+ }
+ if(verbosity>0) std::cout <<"denom: " << dDenom<< std::endl;
+-if( dDenom < std::numeric_limits::epsilon() * 100 ||
isnan(dDenom)) return;
++if( dDenom < std::numeric_limits::epsilon() * 100 ||
std::isnan(dDenom)) return;
+ ForceAssert(dDenom>0);
+ if(verbosity>0){
+ for( uint64_t row=0;row
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/
commit: 0a3000eaaa11495660b9def7f37f87c8f2f23c81
Author: David Seifert gentoo org>
AuthorDate: Sun Jan 17 10:43:48 2016 +
Commit: David Seifert gentoo org>
CommitDate: Sun Jan 17 10:52:24 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0a3000ea
sci-biology/allpathslg: Add blocking packages to RDEPEND too
Package-Manager: portage-2.2.26
...llpathslg-52488.ebuild => allpathslg-52488-r1.ebuild} | 16 ++--
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/sci-biology/allpathslg/allpathslg-52488.ebuild
b/sci-biology/allpathslg/allpathslg-52488-r1.ebuild
similarity index 82%
rename from sci-biology/allpathslg/allpathslg-52488.ebuild
rename to sci-biology/allpathslg/allpathslg-52488-r1.ebuild
index 4518cac..268d759 100644
--- a/sci-biology/allpathslg/allpathslg-52488.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52488-r1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=6
-inherit autotools eutils flag-o-matic
+inherit autotools flag-o-matic
DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
@@ -16,13 +16,17 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE="openmp"
-DEPEND="
- dev-libs/boost
+RDEPEND="
!sci-biology/allpaths
!sci-biology/vaal"
-RDEPEND=""
+DEPEND="
+ ${RDEPEND}
+ dev-libs/boost"
-PATCHES=("${FILESDIR}/${P}_fix-buildsystem.patch"
"${FILESDIR}/${P}_remove-namespace-std.patch")
+PATCHES=(
+ "${FILESDIR}/${P}_fix-buildsystem.patch"
+ "${FILESDIR}/${P}_remove-namespace-std.patch"
+)
pkg_pretend() {
# as of release 44849, GCC 4.7.0 (or higher) is required
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/
commit: e4bde0761cc5d8b21d7f9d7d40145a3fa160e384
Author: Justin Lecher gentoo org>
AuthorDate: Tue Dec 29 11:35:53 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Tue Dec 29 11:36:00 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4bde076
sci-biology/allpathslg: Block sci-biology/vaal as it is nicluded in this release
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=570070
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher gentoo.org>
sci-biology/allpathslg/allpathslg-52488.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/allpathslg/allpathslg-52488.ebuild
b/sci-biology/allpathslg/allpathslg-52488.ebuild
index effa25c..4518cac 100644
--- a/sci-biology/allpathslg/allpathslg-52488.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52488.ebuild
@@ -19,7 +19,7 @@ IUSE="openmp"
DEPEND="
dev-libs/boost
!sci-biology/allpaths
- sci-biology/vaal"
+ !sci-biology/vaal"
RDEPEND=""
PATCHES=("${FILESDIR}/${P}_fix-buildsystem.patch"
"${FILESDIR}/${P}_remove-namespace-std.patch")
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/
commit: 8ebd98c00dd68c1b4ff0aaeb4cadfc1980753655
Author: Justin Lecher gentoo org>
AuthorDate: Wed Dec 23 16:34:43 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Dec 23 18:55:56 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8ebd98c0
sci-biology/allpathslg: Drop old
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher gentoo.org>
sci-biology/allpathslg/Manifest| 2 -
sci-biology/allpathslg/allpathslg-47093.ebuild | 36 -
sci-biology/allpathslg/allpathslg-52415.ebuild | 54 --
3 files changed, 92 deletions(-)
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
index 8db6db4..cd18242 100644
--- a/sci-biology/allpathslg/Manifest
+++ b/sci-biology/allpathslg/Manifest
@@ -1,4 +1,2 @@
DIST allpathslg-42337.tar.gz 2739498 SHA256
a2c8f64f6ba1705b2331ca07761d189183c6745f8717ffc67ee98e9e3ca3dba6 SHA512
7595fbe14a5029578b57d16f781cbb2a0f0ad6b1af2dd770e2274f8fe2e11d0013fdff12cc85c1be748e769ffb23b7d5fe30920feef38e0e8b947d05b8bda31c
WHIRLPOOL
79bda55d49877641eb55630950472a06d8f25db467dbfecde8b4d04c3ce16c071d32dd312fa9a0f72723bf4caa8f9b1d0346acf438b9671b4bed2c0672c788b9
-DIST allpathslg-47093.tar.gz 3057279 SHA256
493e21ae727250ea632b73b61545c32de2d8fb31e6a92605393ebb4af251f828 SHA512
499d23de52cad666fac663eb4a7d770b2129c4f9622f6c808ce30283429b6f67fb343f8712b07c7cb062c429117a0855da960ffc1d2ffb4e7ec2f544ba5a6314
WHIRLPOOL
a3bc58dc140be3cddbd44c7035e628c4425bf86bc38592004df21d4dc91958ced9f08d667b43c15c214e53e3098805f368a856e66e5c2049b0e03d043b098ebc
-DIST allpathslg-52415.tar.gz 3129266 SHA256
3c62024a0eacdc223bc727be4718da644fb302f785c7c7347a09ff422ce96362 SHA512
afe25b07d2e07dee3ced2283ffe858f24acfb35d53e9c11fcbcc47373594453d798c344d5604eb24d5c8d3685a185a3b8807bb3547d8066cbaab8d8cf927d1d6
WHIRLPOOL
de15dfeddeca2f64fd8780839c45096c28cb47ec219d781f6754f9cf65ad6dfc39b8a48aaa2c36f777282fb08ac78ef8cd04c2e1d79f4f797710d3bb38792785
DIST allpathslg-52488.tar.gz 3121949 SHA256
035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542 SHA512
c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d
WHIRLPOOL
c63a13450c55fce8f2c5399bdd5d8f32939e31d9d13a120835b1d826ae96e251fea81caa134d5d45ad857af0777c22e4ad1d894c81a74db6d83a7d9ad83b12b4
diff --git a/sci-biology/allpathslg/allpathslg-47093.ebuild
b/sci-biology/allpathslg/allpathslg-47093.ebuild
deleted file mode 100644
index ab971ec..000
--- a/sci-biology/allpathslg/allpathslg-47093.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools eutils flag-o-matic
-
-DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd;
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz;
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 -x86"
-
-DEPEND="
- dev-libs/boost
- !sci-biology/allpaths
- sci-biology/vaal"
-RDEPEND=""
-
-src_prepare() {
- epatch "${FILESDIR}"/${P}-gcc4.9.patch
- sed -i 's/-ggdb//' configure.ac || die
- eautoreconf
-}
-
-src_install() {
- default
- # Provided by sci-biology/vaal
- for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb
ShortQueryLookup; do
- rm "${ED}/usr/bin/$i" || die
- done
-}
diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild
b/sci-biology/allpathslg/allpathslg-52415.ebuild
deleted file mode 100644
index 29de20e..000
--- a/sci-biology/allpathslg/allpathslg-52415.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils flag-o-matic
-
-DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
-# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd;
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="openmp"
-
-DEPEND="
- dev-libs/boost
- !sci-biology/allpaths
- sci-biology/vaal"
-RDEPEND=""
-
-pkg_pretend() {
- # as of release 44849, GCC 4.7.0 (or higher) is required
- # seems pre gcc-4.7 users must stay with:
- #
ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
- if [[ ${MERGE_TYPE} != binary ]]; then
- [[ $(tc-getCC) == *gcc* ]] && [[ $(gcc-version) < 4.7 ]] && \
- die "You need to use gcc >4.7"
- fi
-}
-
-src_prepare() {
- local i
-
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/files/, sci-biology/allpathslg/
commit: 38789fe4d68d3806961afe972dd89d236a5995df
Author: Ted Tanberry gmail com>
AuthorDate: Wed Dec 23 09:03:29 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Dec 23 16:32:22 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=38789fe4
sci-biology/allpathslg: Version bump and fix bug 568440.
Package-Manager: portage-2.2.26
sci-biology/allpathslg/Manifest|1 +
sci-biology/allpathslg/allpathslg-52488.ebuild | 48 +
.../files/allpathslg-52488_fix-buildsystem.patch | 33 +
.../allpathslg-52488_remove-namespace-std.patch| 1750
4 files changed, 1832 insertions(+)
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest
index 8209935..8db6db4 100644
--- a/sci-biology/allpathslg/Manifest
+++ b/sci-biology/allpathslg/Manifest
@@ -1,3 +1,4 @@
DIST allpathslg-42337.tar.gz 2739498 SHA256
a2c8f64f6ba1705b2331ca07761d189183c6745f8717ffc67ee98e9e3ca3dba6 SHA512
7595fbe14a5029578b57d16f781cbb2a0f0ad6b1af2dd770e2274f8fe2e11d0013fdff12cc85c1be748e769ffb23b7d5fe30920feef38e0e8b947d05b8bda31c
WHIRLPOOL
79bda55d49877641eb55630950472a06d8f25db467dbfecde8b4d04c3ce16c071d32dd312fa9a0f72723bf4caa8f9b1d0346acf438b9671b4bed2c0672c788b9
DIST allpathslg-47093.tar.gz 3057279 SHA256
493e21ae727250ea632b73b61545c32de2d8fb31e6a92605393ebb4af251f828 SHA512
499d23de52cad666fac663eb4a7d770b2129c4f9622f6c808ce30283429b6f67fb343f8712b07c7cb062c429117a0855da960ffc1d2ffb4e7ec2f544ba5a6314
WHIRLPOOL
a3bc58dc140be3cddbd44c7035e628c4425bf86bc38592004df21d4dc91958ced9f08d667b43c15c214e53e3098805f368a856e66e5c2049b0e03d043b098ebc
DIST allpathslg-52415.tar.gz 3129266 SHA256
3c62024a0eacdc223bc727be4718da644fb302f785c7c7347a09ff422ce96362 SHA512
afe25b07d2e07dee3ced2283ffe858f24acfb35d53e9c11fcbcc47373594453d798c344d5604eb24d5c8d3685a185a3b8807bb3547d8066cbaab8d8cf927d1d6
WHIRLPOOL
de15dfeddeca2f64fd8780839c45096c28cb47ec219d781f6754f9cf65ad6dfc39b8a48aaa2c36f777282fb08ac78ef8cd04c2e1d79f4f797710d3bb38792785
+DIST allpathslg-52488.tar.gz 3121949 SHA256
035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542 SHA512
c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d
WHIRLPOOL
c63a13450c55fce8f2c5399bdd5d8f32939e31d9d13a120835b1d826ae96e251fea81caa134d5d45ad857af0777c22e4ad1d894c81a74db6d83a7d9ad83b12b4
diff --git a/sci-biology/allpathslg/allpathslg-52488.ebuild
b/sci-biology/allpathslg/allpathslg-52488.ebuild
new file mode 100644
index 000..0b0b806
--- /dev/null
+++ b/sci-biology/allpathslg/allpathslg-52488.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools eutils flag-o-matic
+
+DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
+# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
+HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd;
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="openmp"
+
+DEPEND="
+ dev-libs/boost
+ !sci-biology/allpaths
+ sci-biology/vaal"
+RDEPEND=""
+
+PATCHES=("${FILESDIR}/${P}_fix-buildsystem.patch"
"${FILESDIR}/${P}_remove-namespace-std.patch")
+
+pkg_pretend() {
+ # as of release 44849, GCC 4.7.0 (or higher) is required
+ # seems pre gcc-4.7 users must stay with:
+ #
ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
+ if [[ ${MERGE_TYPE} != binary ]]; then
+ [[ $(tc-getCC) == *gcc* ]] && [[ $(gcc-version) < 4.7 ]] && \
+ die "You need to use gcc >4.7"
+ fi
+}
+
+src_prepare() {
+ default_src_prepare
+
+ eautoreconf
+}
+
+src_configure() {
+ local myeconfargs=(
+ $(use_enable openmp)
+ )
+ default_src_configure
+}
diff --git
a/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch
b/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch
new file mode 100644
index 000..7944eb5
--- /dev/null
+++ b/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch
@@ -0,0 +1,33 @@
+Fix build system to remove hardcoded debugging flags.
+
+--- allpathslg-52488/configure.ac
allpathslg-52488/configure.ac
+@@ -12,7 +12,7 @@
+ AC_OPENMP
+ AC_OPENMP_CHECK
+
+-CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo
-Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long
-Wno-parentheses -Wno-unused-parameter -fno-nonansi-builtins -mieee-fp
-fno-strict-aliasing -iquote . -ggdb -DNDEBUG"
++CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo
-Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long
-Wno-parentheses
[gentoo-commits] repo/gentoo:master commit in: sci-biology/allpathslg/
commit: c448e05dda73f7f3376ed3bf28de34bf109ac6bb
Author: Justin Lecher gentoo org>
AuthorDate: Wed Dec 23 16:22:51 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Wed Dec 23 16:32:22 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c448e05d
sci-biology/allpathslg: default_src_configure doesn't support myeconfargs
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher gentoo.org>
sci-biology/allpathslg/allpathslg-52488.ebuild | 6 ++
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/sci-biology/allpathslg/allpathslg-52488.ebuild
b/sci-biology/allpathslg/allpathslg-52488.ebuild
index 0b0b806..effa25c 100644
--- a/sci-biology/allpathslg/allpathslg-52488.ebuild
+++ b/sci-biology/allpathslg/allpathslg-52488.ebuild
@@ -35,14 +35,12 @@ pkg_pretend() {
}
src_prepare() {
- default_src_prepare
+ default
eautoreconf
}
src_configure() {
- local myeconfargs=(
+ econf \
$(use_enable openmp)
- )
- default_src_configure
}
