* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2016-02-08 23:34 Sergei Trofimovich
0 siblings, 0 replies; 14+ messages in thread
From: Sergei Trofimovich @ 2016-02-08 23:34 UTC (permalink / raw
To: gentoo-commits
commit: a50e1769e82e28dedb16083ac9136f17f9af2297
Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 8 23:33:45 2016 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Mon Feb 8 23:33:55 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a50e1769
sci-biology/abyss: fix automagic haskell deps, bug #534412
Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/534412
Package-Manager: portage-2.2.27
sci-biology/abyss/abyss-1.3.6.ebuild | 19 +++++++++++++++----
sci-biology/abyss/metadata.xml | 7 +++++++
2 files changed, 22 insertions(+), 4 deletions(-)
diff --git a/sci-biology/abyss/abyss-1.3.6.ebuild b/sci-biology/abyss/abyss-1.3.6.ebuild
index 04dcc7c..904b3e1 100644
--- a/sci-biology/abyss/abyss-1.3.6.ebuild
+++ b/sci-biology/abyss/abyss-1.3.6.ebuild
@@ -14,14 +14,21 @@ SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
LICENSE="abyss"
SLOT="0"
-IUSE="+mpi openmp"
+IUSE="+mpi openmp misc-haskell"
KEYWORDS="~amd64 ~x86"
-DEPEND="
+RDEPEND="
dev-cpp/sparsehash
dev-libs/boost
- mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
+ misc-haskell? ( dev-libs/gmp:0=
+ virtual/libffi:0=
+ )
+ mpi? ( virtual/mpi )
+"
+DEPEND="${RDEPEND}
+ misc-haskell? ( dev-lang/ghc
+ dev-haskell/mmap )
+"
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
@@ -39,6 +46,10 @@ src_prepare() {
}
src_configure() {
+ # disable building haskell tool Misc/samtobreak
+ # unless request by user: bug #534412
+ use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
local myeconfargs=(
--docdir="${EPREFIX}/usr/share/doc/${PF}"
$(use_enable openmp)
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
index 959160f..c0c84f0 100644
--- a/sci-biology/abyss/metadata.xml
+++ b/sci-biology/abyss/metadata.xml
@@ -5,4 +5,11 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <maintainer type="project">
+ <email>haskell@gentoo.org</email>
+ <name>Gentoo Haskell</name>
+ </maintainer>
+ <use>
+ <flag name='misc-haskell'>build abyss-samtobreak tool, pull in haskell toolchain</flag>
+ </use>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2016-05-15 8:26 Sergei Trofimovich
0 siblings, 0 replies; 14+ messages in thread
From: Sergei Trofimovich @ 2016-05-15 8:26 UTC (permalink / raw
To: gentoo-commits
commit: f5f3cc796d91c55aaba42ad00ffb441379848a3b
Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Sun May 15 08:25:43 2016 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Sun May 15 08:25:54 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f5f3cc79
sci-biology/abyss: add missing dev-libs/boost dependency
Package-Manager: portage-2.2.28
sci-biology/abyss/abyss-1.3.3.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/abyss/abyss-1.3.3.ebuild b/sci-biology/abyss/abyss-1.3.3.ebuild
index 08a82e2..62b79f6 100644
--- a/sci-biology/abyss/abyss-1.3.3.ebuild
+++ b/sci-biology/abyss/abyss-1.3.3.ebuild
@@ -17,6 +17,7 @@ KEYWORDS="amd64 x86"
DEPEND="
dev-cpp/sparsehash
+ dev-libs/boost
mpi? ( virtual/mpi )"
RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2016-09-18 22:51 Sergei Trofimovich
0 siblings, 0 replies; 14+ messages in thread
From: Sergei Trofimovich @ 2016-09-18 22:51 UTC (permalink / raw
To: gentoo-commits
commit: 3602af844edaa72d2e2e62018e61466fa3117a51
Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 18 22:51:40 2016 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Sun Sep 18 22:51:40 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3602af84
sci-biology/abyss: pin boost subslot, noticed by Soap
Package-Manager: portage-2.3.0
sci-biology/abyss/{abyss-1.9.0.ebuild => abyss-1.9.0-r1.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild b/sci-biology/abyss/abyss-1.9.0-r1.ebuild
similarity index 98%
rename from sci-biology/abyss/abyss-1.9.0.ebuild
rename to sci-biology/abyss/abyss-1.9.0-r1.ebuild
index c32b477..da80168 100644
--- a/sci-biology/abyss/abyss-1.9.0.ebuild
+++ b/sci-biology/abyss/abyss-1.9.0-r1.ebuild
@@ -17,7 +17,7 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-cpp/sparsehash
- dev-libs/boost
+ dev-libs/boost:=
misc-haskell? ( dev-libs/gmp:0=
virtual/libffi:0=
)
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2016-11-06 13:12 Sergei Trofimovich
0 siblings, 0 replies; 14+ messages in thread
From: Sergei Trofimovich @ 2016-11-06 13:12 UTC (permalink / raw
To: gentoo-commits
commit: 4c8a5799cd9b07143e1c1b9ba865c3e9bbbf5f3e
Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 6 13:12:25 2016 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Sun Nov 6 13:12:25 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4c8a5799
sci-biology/abyss: bump up to 2.0.2, bug #596018
Fixes gcc-6 and boost-1.62 build failures.
Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/596018
Package-Manager: portage-2.3.2
sci-biology/abyss/Manifest | 1 +
sci-biology/abyss/abyss-1.9.0-r1.ebuild | 2 +-
sci-biology/abyss/{abyss-1.9.0-r1.ebuild => abyss-2.0.2.ebuild} | 8 +-------
3 files changed, 3 insertions(+), 8 deletions(-)
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index e995775..f19563b 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,3 +1,4 @@
DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914
DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07
DIST abyss-1.9.0.tar.gz 985480 SHA256 82e4050766a9c7fb87fd736f94724a02388efb1df847b40870a0fbf842917239 SHA512 d9da19f004bb97f9301f3be83ceb5361eb70f42139a1ef17129de99e03bda5de7680d718d76aed26d26f24c1d26c37e050801ff343acad007b76d2214955b83f WHIRLPOOL bd322afa9bf99a53aec177c79ca9618f39043cda606eb4e3d5dcfb46c26298d218fc154e2c46efadac59febb69dd625fe597101a1efbccc62ab8228b555596cc
+DIST abyss-2.0.2.tar.gz 1036135 SHA256 6482b81eb5439703c0dbf6cd7ac25cd0df7541d9e04ef7865343b241e21db460 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30 WHIRLPOOL 23447cb00b0bb9b5b8a724ba44f8d7193d9640ccd19956b42bbbd83b67557b66b7c68141d6f292c4ab11ab523286471d5ee1c938f22749a61162de056a0d903e
diff --git a/sci-biology/abyss/abyss-1.9.0-r1.ebuild b/sci-biology/abyss/abyss-1.9.0-r1.ebuild
index da80168..32af453 100644
--- a/sci-biology/abyss/abyss-1.9.0-r1.ebuild
+++ b/sci-biology/abyss/abyss-1.9.0-r1.ebuild
@@ -8,7 +8,7 @@ inherit autotools toolchain-funcs
DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="abyss"
SLOT="0"
diff --git a/sci-biology/abyss/abyss-1.9.0-r1.ebuild b/sci-biology/abyss/abyss-2.0.2.ebuild
similarity index 86%
copy from sci-biology/abyss/abyss-1.9.0-r1.ebuild
copy to sci-biology/abyss/abyss-2.0.2.ebuild
index da80168..92a3780 100644
--- a/sci-biology/abyss/abyss-1.9.0-r1.ebuild
+++ b/sci-biology/abyss/abyss-2.0.2.ebuild
@@ -8,7 +8,7 @@ inherit autotools toolchain-funcs
DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="abyss"
SLOT="0"
@@ -31,14 +31,8 @@ DEPEND="${RDEPEND}
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
-PATCHES=(
- "${FILESDIR}"/${P}-ac_prog_ar.patch
- "${FILESDIR}"/${P}-gcc-6.patch
-)
-
src_prepare() {
default
- tc-export AR
sed -i -e "s/-Werror//" configure.ac || die #365195
sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
eautoreconf
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2017-01-15 17:54 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2017-01-15 17:54 UTC (permalink / raw
To: gentoo-commits
commit: 6764ffe099c90b89117afeb0087258ec76f3136f
Author: Martin Mokrejš <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Tue Jan 10 13:32:37 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jan 15 17:53:17 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6764ffe0
sci-biology/abyss: only openmpi is supported
Closes: https://github.com/gentoo/gentoo/pull/3414
.../{abyss-2.0.2.ebuild => abyss-2.0.2-r1.ebuild} | 23 +++++++++++++++-------
1 file changed, 16 insertions(+), 7 deletions(-)
diff --git a/sci-biology/abyss/abyss-2.0.2.ebuild b/sci-biology/abyss/abyss-2.0.2-r1.ebuild
similarity index 75%
rename from sci-biology/abyss/abyss-2.0.2.ebuild
rename to sci-biology/abyss/abyss-2.0.2-r1.ebuild
index 92a3780..4533f9b 100644
--- a/sci-biology/abyss/abyss-2.0.2.ebuild
+++ b/sci-biology/abyss/abyss-2.0.2-r1.ebuild
@@ -18,19 +18,28 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-cpp/sparsehash
dev-libs/boost:=
- misc-haskell? ( dev-libs/gmp:0=
- virtual/libffi:0=
+ misc-haskell? (
+ dev-libs/gmp:0=
+ virtual/libffi:0=
)
- mpi? ( virtual/mpi )
-"
+ mpi? ( sys-cluster/openmpi )"
DEPEND="${RDEPEND}
- misc-haskell? ( dev-lang/ghc
- dev-haskell/mmap )
-"
+ misc-haskell? (
+ dev-lang/ghc
+ dev-haskell/mmap
+ )"
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
+pkg_pretend() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
src_prepare() {
default
sed -i -e "s/-Werror//" configure.ac || die #365195
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2018-03-15 23:33 Sergei Trofimovich
0 siblings, 0 replies; 14+ messages in thread
From: Sergei Trofimovich @ 2018-03-15 23:33 UTC (permalink / raw
To: gentoo-commits
commit: 42bcef7f16f3999182b38951f69ce0e15d1ef58a
Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 15 23:30:40 2018 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Thu Mar 15 23:33:14 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=42bcef7f
sci-biology/abyss: bump up to 2.0.3
Package-Manager: Portage-2.3.24, Repoman-2.3.6
sci-biology/abyss/Manifest | 1 +
sci-biology/abyss/abyss-2.0.3.ebuild | 54 ++++++++++++++++++++++++++++++++++++
2 files changed, 55 insertions(+)
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index 20d851c721d..b18ccd65238 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1 +1,2 @@
DIST abyss-2.0.2.tar.gz 1036135 BLAKE2B 6781a63203b5e6a1de70837a6dad7c79643d049b4c1e4b827471f2414cc821f82d98f9856518e3c24486e068c584520d0a1852d4e03d26247b896c776baaee41 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30
+DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570
diff --git a/sci-biology/abyss/abyss-2.0.3.ebuild b/sci-biology/abyss/abyss-2.0.3.ebuild
new file mode 100644
index 00000000000..ccce937c77c
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.0.3.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost:=
+ misc-haskell? (
+ dev-libs/gmp:0=
+ virtual/libffi:0=
+ )
+ mpi? ( sys-cluster/openmpi )"
+DEPEND="${RDEPEND}
+ misc-haskell? (
+ dev-lang/ghc
+ )"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+pkg_pretend() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+ default
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ eautoreconf
+}
+
+src_configure() {
+ # disable building haskell tool Misc/samtobreak
+ # unless request by user: bug #534412
+ use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
+ econf $(use_enable openmp)
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2020-05-25 10:56 Sergei Trofimovich
0 siblings, 0 replies; 14+ messages in thread
From: Sergei Trofimovich @ 2020-05-25 10:56 UTC (permalink / raw
To: gentoo-commits
commit: caf207dd9d6bdc71885f9f459625856665972df1
Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Mon May 25 10:55:52 2020 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Mon May 25 10:55:52 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=caf207dd
sci-biology/abyss: disable CFLAGS QA check on samtobreak
GHC uses it's own native code generator. Portage's
QA check generates false positive because it assumes
presence of GCC-specific sections.
Workaround false positiove by disabling the check, bug #677600.
Bug: https://bugs.gentoo.org/677600
Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Sergei Trofimovich <slyfox <AT> gentoo.org>
sci-biology/abyss/abyss-2.0.3-r1.ebuild | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/sci-biology/abyss/abyss-2.0.3-r1.ebuild b/sci-biology/abyss/abyss-2.0.3-r1.ebuild
index 6c8571fafa6..800a45964cd 100644
--- a/sci-biology/abyss/abyss-2.0.3-r1.ebuild
+++ b/sci-biology/abyss/abyss-2.0.3-r1.ebuild
@@ -29,6 +29,14 @@ DEPEND="${RDEPEND}
PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch)
+# GHC uses it's own native code generator. Portage's
+# QA check generates false positive because it assumes
+# presence of GCC-specific sections.
+#
+# Workaround false positiove by disabling the check completely.
+# bug #677600
+QA_FLAGS_IGNORED='/usr/bin/abyss-samtobreak'
+
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2020-06-21 10:36 Sergei Trofimovich
0 siblings, 0 replies; 14+ messages in thread
From: Sergei Trofimovich @ 2020-06-21 10:36 UTC (permalink / raw
To: gentoo-commits
commit: 2007740170c55928a8e0d7f5f0628f58f3234c5b
Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 10:35:24 2020 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 10:35:24 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=20077401
sci-biology/abyss: drop old
Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: Sergei Trofimovich <slyfox <AT> gentoo.org>
sci-biology/abyss/Manifest | 1 -
sci-biology/abyss/abyss-2.0.2-r1.ebuild | 55 ---------------------------------
sci-biology/abyss/abyss-2.0.3.ebuild | 54 --------------------------------
3 files changed, 110 deletions(-)
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index b18ccd65238..e03409dd93f 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,2 +1 @@
-DIST abyss-2.0.2.tar.gz 1036135 BLAKE2B 6781a63203b5e6a1de70837a6dad7c79643d049b4c1e4b827471f2414cc821f82d98f9856518e3c24486e068c584520d0a1852d4e03d26247b896c776baaee41 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30
DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570
diff --git a/sci-biology/abyss/abyss-2.0.2-r1.ebuild b/sci-biology/abyss/abyss-2.0.2-r1.ebuild
deleted file mode 100644
index 0d1c14ac265..00000000000
--- a/sci-biology/abyss/abyss-2.0.2-r1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost:=
- misc-haskell? (
- dev-libs/gmp:0=
- virtual/libffi:0=
- )
- mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
- misc-haskell? (
- dev-lang/ghc
- dev-haskell/mmap
- )"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
- default
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- # disable building haskell tool Misc/samtobreak
- # unless request by user: bug #534412
- use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
- econf $(use_enable openmp)
-}
diff --git a/sci-biology/abyss/abyss-2.0.3.ebuild b/sci-biology/abyss/abyss-2.0.3.ebuild
deleted file mode 100644
index ccce937c77c..00000000000
--- a/sci-biology/abyss/abyss-2.0.3.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost:=
- misc-haskell? (
- dev-libs/gmp:0=
- virtual/libffi:0=
- )
- mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
- misc-haskell? (
- dev-lang/ghc
- )"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
- default
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- # disable building haskell tool Misc/samtobreak
- # unless request by user: bug #534412
- use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
- econf $(use_enable openmp)
-}
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2020-06-21 16:47 Sergei Trofimovich
0 siblings, 0 replies; 14+ messages in thread
From: Sergei Trofimovich @ 2020-06-21 16:47 UTC (permalink / raw
To: gentoo-commits
commit: 4499edbc478106c4f7a04062c8ee2f273474c8cb
Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 16:46:53 2020 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 16:47:16 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4499edbc
sci-biology/abyss: switch from virtual/libffi
Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: Sergei Trofimovich <slyfox <AT> gentoo.org>
sci-biology/abyss/{abyss-2.0.3-r1.ebuild => abyss-2.0.3-r2.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/abyss/abyss-2.0.3-r1.ebuild b/sci-biology/abyss/abyss-2.0.3-r2.ebuild
similarity index 98%
rename from sci-biology/abyss/abyss-2.0.3-r1.ebuild
rename to sci-biology/abyss/abyss-2.0.3-r2.ebuild
index 800a45964cd..b9aed09d3ee 100644
--- a/sci-biology/abyss/abyss-2.0.3-r1.ebuild
+++ b/sci-biology/abyss/abyss-2.0.3-r2.ebuild
@@ -19,7 +19,7 @@ RDEPEND="
dev-libs/boost:=
misc-haskell? (
dev-libs/gmp:0=
- virtual/libffi:0=
+ dev-libs/libffi:0=
)
mpi? ( sys-cluster/openmpi )"
DEPEND="${RDEPEND}
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2021-07-24 10:09 Sergei Trofimovich
0 siblings, 0 replies; 14+ messages in thread
From: Sergei Trofimovich @ 2021-07-24 10:09 UTC (permalink / raw
To: gentoo-commits
commit: 175bb6cfefa4711aa556ba93463b861659ffbeda
Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 24 10:09:05 2021 +0000
Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org>
CommitDate: Sat Jul 24 10:09:05 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=175bb6cf
sci-biology/abyss: drop haskell@ from maintainers
Package-Manager: Portage-3.0.20, Repoman-3.0.3
Signed-off-by: Sergei Trofimovich <slyfox <AT> gentoo.org>
sci-biology/abyss/metadata.xml | 4 ----
1 file changed, 4 deletions(-)
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
index 2a6a2c73d6a..a4fc7944c7d 100644
--- a/sci-biology/abyss/metadata.xml
+++ b/sci-biology/abyss/metadata.xml
@@ -5,10 +5,6 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
- <maintainer type="project">
- <email>haskell@gentoo.org</email>
- <name>Gentoo Haskell</name>
- </maintainer>
<use>
<flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag>
</use>
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2022-01-13 11:21 Andrew Ammerlaan
0 siblings, 0 replies; 14+ messages in thread
From: Andrew Ammerlaan @ 2022-01-13 11:21 UTC (permalink / raw
To: gentoo-commits
commit: 03ada3844855dd1c9ff2627e7f9239d0248e7cc6
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 13 11:19:37 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Jan 13 11:21:36 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=03ada384
sci-biology/abyss: add version 2.3.4
Closes: https://bugs.gentoo.org/646478
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/abyss/Manifest | 1 +
sci-biology/abyss/abyss-2.3.4.ebuild | 57 ++++++++++++++++++++++++++++++++++++
2 files changed, 58 insertions(+)
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index e03409dd93f2..32cead3a3a6e 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1 +1,2 @@
DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570
+DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4
diff --git a/sci-biology/abyss/abyss-2.3.4.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild
new file mode 100644
index 000000000000..c2e1ffd29b32
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.3.4.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/"
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost:=
+ misc-haskell? (
+ dev-libs/gmp:0=
+ dev-libs/libffi:0=
+ )
+ sys-cluster/openmpi
+ dev-db/sqlite:3
+"
+DEPEND="${RDEPEND}
+ misc-haskell? (
+ dev-lang/ghc
+ )
+"
+
+# todo: --enable-maxk=N configure option
+# todo: also allow build with mpich (--enable-mpich)
+
+pkg_pretend() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+ default
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ eautoreconf
+}
+
+src_configure() {
+ # disable building haskell tool Misc/samtobreak
+ # unless request by user: bug #534412
+ use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
+ econf $(use_enable openmp) --enable-maxk=256
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2022-07-30 8:31 Sam James
0 siblings, 0 replies; 14+ messages in thread
From: Sam James @ 2022-07-30 8:31 UTC (permalink / raw
To: gentoo-commits
commit: 2f84b4653122a67060b792372e8c52da4d8a5d4b
Author: Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 30 08:27:55 2022 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Jul 30 08:27:55 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2f84b465
sci-biology/abyss: fix metadata indentation
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/abyss/metadata.xml | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
index 23a340ee3255..04e203d593eb 100644
--- a/sci-biology/abyss/metadata.xml
+++ b/sci-biology/abyss/metadata.xml
@@ -1,14 +1,14 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <use>
- <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag>
- </use>
- <upstream>
- <remote-id type="github">bcgsc/abyss</remote-id>
- </upstream>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <use>
+ <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag>
+ </use>
+ <upstream>
+ <remote-id type="github">bcgsc/abyss</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2024-03-08 11:09 Sam James
0 siblings, 0 replies; 14+ messages in thread
From: Sam James @ 2024-03-08 11:09 UTC (permalink / raw
To: gentoo-commits
commit: d0b8036f8b6c998f0cd1f5f975e04ec61d2cfe9f
Author: Eli Schwartz <eschwartz93 <AT> gmail <DOT> com>
AuthorDate: Fri Mar 8 01:06:32 2024 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Fri Mar 8 11:09:00 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d0b8036f
sci-biology/abyss: remove useless sed
It seds out something that hasn't existed since 2012:
https://github.com/bcgsc/abyss/commit/ded065d3b257e72ceb70ad3f6dd399019b00b46e
Signed-off-by: Eli Schwartz <eschwartz93 <AT> gmail.com>
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/abyss/abyss-2.3.4.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/abyss/abyss-2.3.4.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild
index c2e1ffd29b32..437975eb357a 100644
--- a/sci-biology/abyss/abyss-2.3.4.ebuild
+++ b/sci-biology/abyss/abyss-2.3.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -44,7 +44,6 @@ pkg_setup() {
src_prepare() {
default
sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
eautoreconf
}
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/
@ 2024-03-08 11:09 Sam James
0 siblings, 0 replies; 14+ messages in thread
From: Sam James @ 2024-03-08 11:09 UTC (permalink / raw
To: gentoo-commits
commit: 490ada295187ec9b28e867128b53f6bdf5f68f63
Author: Eli Schwartz <eschwartz93 <AT> gmail <DOT> com>
AuthorDate: Fri Mar 8 01:20:48 2024 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Fri Mar 8 11:09:00 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=490ada29
sci-biology/abyss: mark as LTO-unsafe
Closes: https://bugs.gentoo.org/862252
Signed-off-by: Eli Schwartz <eschwartz93 <AT> gmail.com>
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-biology/abyss/abyss-2.3.4.ebuild | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-biology/abyss/abyss-2.3.4.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild
index 437975eb357a..2c2c14d35bd5 100644
--- a/sci-biology/abyss/abyss-2.3.4.ebuild
+++ b/sci-biology/abyss/abyss-2.3.4.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-inherit autotools toolchain-funcs
+inherit autotools flag-o-matic toolchain-funcs
DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/"
@@ -48,6 +48,11 @@ src_prepare() {
}
src_configure() {
+ # -Werror=lto-type-mismatch
+ # https://bugs.gentoo.org/862252
+ # https://github.com/bcgsc/abyss/issues/474
+ filter-lto
+
# disable building haskell tool Misc/samtobreak
# unless request by user: bug #534412
use misc-haskell || export ac_cv_prog_ac_ct_GHC=
^ permalink raw reply related [flat|nested] 14+ messages in thread
end of thread, other threads:[~2024-03-08 11:09 UTC | newest]
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2018-03-15 23:33 Sergei Trofimovich
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