* [gentoo-commits] repo/gentoo:master commit in: sci-biology/express/
@ 2017-02-08 11:36 Johannes Huber
0 siblings, 0 replies; 5+ messages in thread
From: Johannes Huber @ 2017-02-08 11:36 UTC (permalink / raw
To: gentoo-commits
commit: c6ab3d3efa5f0b10bc6070967a2f435156488b32
Author: Johannes Huber <johu <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 8 11:35:54 2017 +0000
Commit: Johannes Huber <johu <AT> gentoo <DOT> org>
CommitDate: Wed Feb 8 11:36:27 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c6ab3d3e
sci-biology/express: Remove 0.9.5 (r0)
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/express/express-0.9.5.ebuild | 35 --------------------------------
1 file changed, 35 deletions(-)
diff --git a/sci-biology/express/express-0.9.5.ebuild b/sci-biology/express/express-0.9.5.ebuild
deleted file mode 100644
index a4fcff4be4..0000000000
--- a/sci-biology/express/express-0.9.5.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit cmake-utils
-
-DESCRIPTION="Streaming RNA-Seq Analysis"
-HOMEPAGE="http://bio.math.berkeley.edu/eXpress/"
-SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/express-${PV}/express-${PV}-src.tgz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
- dev-libs/boost
- sys-libs/zlib
- sci-biology/bamtools"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${P}-src"
-
-CMAKE_USE_DIR="${S}/src"
-
-src_prepare() {
- sed \
- -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \
- -e '1 a find_package(Boost 1.46 COMPONENTS filesystem program_options thread)' \
- -e '1 a find_package(ZLIB)' \
- -e '/add_executable/ a include_directories("/usr/include/bamtools")' \
- -i src/CMakeLists.txt || die
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/express/
@ 2018-10-14 16:34 Andreas Sturmlechner
0 siblings, 0 replies; 5+ messages in thread
From: Andreas Sturmlechner @ 2018-10-14 16:34 UTC (permalink / raw
To: gentoo-commits
commit: fad62bd824b9ea69a19200061544567eb9e78730
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 14 16:30:19 2018 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sun Oct 14 16:34:29 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fad62bd8
sci-biology/express: Drop old
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
Package-Manager: Portage-2.3.51, Repoman-2.3.11
sci-biology/express/Manifest | 1 -
sci-biology/express/express-0.9.5-r1.ebuild | 35 -----------------------------
2 files changed, 36 deletions(-)
diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest
index 2e05adafed7..9c2cc4ebf49 100644
--- a/sci-biology/express/Manifest
+++ b/sci-biology/express/Manifest
@@ -1,2 +1 @@
-DIST express-0.9.5-src.tgz 766024 BLAKE2B 3818bc9de30a5201d587d3e18feee85f3014b68672eaef32ce0fa5989e0ce2cd7ee8bb8c617db0cde2d061db0f31ba76c49aa03f66be92c40826a6ede35ebca9 SHA512 3a7360ffbe57f4f712b6db38d551d31384d995050a86238d79299edb12f0e7f5dca6f362b7858b5051ea2879af2b3559f78f9780d75ef2ef6fdad7398f781403
DIST express-1.5.1-src.tgz 931166 BLAKE2B 5eb185e4b001f26f0dd32885b256b9fa48c89f546d67d7f8472cade69dde25375a5fc8efed5f01b615d63b641b674f7034a13f9483eb7967a6fd784a55c8878e SHA512 59cf6511a879311247c65334285ea056d571d4fd950aa6243041fa10075ff0d1ddd2afbcfe12e5f7f3e7cdd22fe37fd7f6b43ed4a8eb28d7a33d72366dc549ee
diff --git a/sci-biology/express/express-0.9.5-r1.ebuild b/sci-biology/express/express-0.9.5-r1.ebuild
deleted file mode 100644
index 945398a17a8..00000000000
--- a/sci-biology/express/express-0.9.5-r1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="Streaming RNA-Seq Analysis"
-HOMEPAGE="http://bio.math.berkeley.edu/eXpress/"
-SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/express-${PV}/express-${PV}-src.tgz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- >=dev-libs/boost-1.52.0:=
- sys-libs/zlib
- sci-biology/bamtools"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${P}-src"
-
-CMAKE_USE_DIR="${S}/src"
-
-src_prepare() {
- sed \
- -e 's|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \
- -e '1 a find_package(Boost 1.52 COMPONENTS filesystem program_options system thread)' \
- -e '1 a find_package(ZLIB)' \
- -e '/add_executable/ a include_directories("/usr/include/bamtools")' \
- -i src/CMakeLists.txt || die
-
- cmake-utils_src_prepare
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/express/
@ 2018-10-14 16:34 Andreas Sturmlechner
0 siblings, 0 replies; 5+ messages in thread
From: Andreas Sturmlechner @ 2018-10-14 16:34 UTC (permalink / raw
To: gentoo-commits
commit: 2e39fa5d652b78dfd2d3fb38f2165e6e358dd587
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 14 16:29:31 2018 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sun Oct 14 16:34:29 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2e39fa5d
sci-biology/express: EAPI-6 bump
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
Package-Manager: Portage-2.3.51, Repoman-2.3.11
sci-biology/express/express-1.5.1.ebuild | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild
index 62e5361f529..148df8a8ce1 100644
--- a/sci-biology/express/express-1.5.1.ebuild
+++ b/sci-biology/express/express-1.5.1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
inherit cmake-utils
@@ -18,8 +18,9 @@ DEPEND="
>=dev-libs/boost-1.52.0:=
dev-libs/protobuf
dev-util/google-perftools
+ sci-biology/bamtools
sys-libs/zlib
- sci-biology/bamtools"
+"
RDEPEND="${DEPEND}"
S="${WORKDIR}/${P}-src"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/express/
@ 2021-03-07 19:02 Andreas Sturmlechner
0 siblings, 0 replies; 5+ messages in thread
From: Andreas Sturmlechner @ 2021-03-07 19:02 UTC (permalink / raw
To: gentoo-commits
commit: f2884a9364159fef2f3dc686ed00ce315088661a
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 6 19:32:53 2021 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sun Mar 7 19:01:10 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f2884a93
sci-biology/express: EAPI-7/cmake.eclass, new HOMEPAGE/SRC_URI
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
sci-biology/express/express-1.5.1.ebuild | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild
index 148df8a8ce1..0f8fdce7bbb 100644
--- a/sci-biology/express/express-1.5.1.ebuild
+++ b/sci-biology/express/express-1.5.1.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit cmake-utils
+inherit cmake
DESCRIPTION="Streaming RNA-Seq Analysis"
-HOMEPAGE="http://bio.math.berkeley.edu/eXpress/"
-SRC_URI="http://bio.math.berkeley.edu/eXpress/downloads/${P}/${P}-src.tgz"
+HOMEPAGE="https://pachterlab.github.io/eXpress/"
+SRC_URI="https://pachterlab.github.io/eXpress/downloads/${P}/${P}-src.tgz"
LICENSE="Artistic"
SLOT="0"
@@ -34,5 +34,5 @@ src_configure() {
local mycmakeargs=(
-DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools"
)
- cmake-utils_src_configure
+ cmake_src_configure
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/express/
@ 2022-09-04 13:03 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2022-09-04 13:03 UTC (permalink / raw
To: gentoo-commits
commit: 4fd2ac9cbf5106e0a2997c99b7c43668128b67ad
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 4 13:03:25 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Sep 4 13:03:25 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4fd2ac9c
sci-biology/express: remove stale boost lower bounds
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/express/express-1.5.1.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild
index 0f8fdce7bbb0..9511236b69f6 100644
--- a/sci-biology/express/express-1.5.1.ebuild
+++ b/sci-biology/express/express-1.5.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -15,7 +15,7 @@ KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="
- >=dev-libs/boost-1.52.0:=
+ dev-libs/boost:=
dev-libs/protobuf
dev-util/google-perftools
sci-biology/bamtools
^ permalink raw reply related [flat|nested] 5+ messages in thread
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