[gentoo-commits] repo/gentoo:master commit in: sci-biology/express/, sci-biology/express/files/, profiles/
commit: 9dd02118b6f0149e41c814e40876e45481112148
Author: Florian Schmaus gentoo org>
AuthorDate: Mon Oct 2 11:29:13 2023 +
Commit: Florian Schmaus gentoo org>
CommitDate: Mon Oct 2 11:36:49 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9dd02118
sci-biology/express: treeclean
Closes: https://bugs.gentoo.org/912828
Signed-off-by: Florian Schmaus gentoo.org>
profiles/package.mask | 6 ---
sci-biology/express/Manifest | 1 -
sci-biology/express/express-1.5.1.ebuild | 38 ---
.../express/files/express-1.5.1-buildsystem.patch | 55 --
sci-biology/express/files/express-1.5.1-gcc6.patch | 19
sci-biology/express/metadata.xml | 8
6 files changed, 127 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index e616cfe60492..647fbfd7c812 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -260,12 +260,6 @@ dev-ruby/twitter:7
# Removal on 2023-09-28. Bug #830477, bug #913004.
net-im/ricochet
-# Sam James (2023-08-29)
-# Fails to build with new protobuf. Deprecated by upstream which recommend
-# sci-biology/kallisto as a replacement.
-# Removal on 2023-09-28. Bug #912828.
-sci-biology/express
-
# Sam James (2023-08-04)
# Stricter behavior which causes some packages to fail, see bug #911721.
=dev-util/pkgconf-2.0.0
diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest
deleted file mode 100644
index 9c2cc4ebf499..
--- a/sci-biology/express/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST express-1.5.1-src.tgz 931166 BLAKE2B
5eb185e4b001f26f0dd32885b256b9fa48c89f546d67d7f8472cade69dde25375a5fc8efed5f01b615d63b641b674f7034a13f9483eb7967a6fd784a55c8878e
SHA512
59cf6511a879311247c65334285ea056d571d4fd950aa6243041fa10075ff0d1ddd2afbcfe12e5f7f3e7cdd22fe37fd7f6b43ed4a8eb28d7a33d72366dc549ee
diff --git a/sci-biology/express/express-1.5.1.ebuild
b/sci-biology/express/express-1.5.1.ebuild
deleted file mode 100644
index 9511236b69f6..
--- a/sci-biology/express/express-1.5.1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Streaming RNA-Seq Analysis"
-HOMEPAGE="https://pachterlab.github.io/eXpress/;
-SRC_URI="https://pachterlab.github.io/eXpress/downloads/${P}/${P}-src.tgz;
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
- dev-libs/boost:=
- dev-libs/protobuf
- dev-util/google-perftools
- sci-biology/bamtools
- sys-libs/zlib
-"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${P}-src"
-
-PATCHES=(
- "${FILESDIR}"/${P}-buildsystem.patch
- "${FILESDIR}"/${P}-gcc6.patch
-)
-
-src_configure() {
- local mycmakeargs=(
- -DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools"
- )
- cmake_src_configure
-}
diff --git a/sci-biology/express/files/express-1.5.1-buildsystem.patch
b/sci-biology/express/files/express-1.5.1-buildsystem.patch
deleted file mode 100644
index fca5feadd111..
--- a/sci-biology/express/files/express-1.5.1-buildsystem.patch
+++ /dev/null
@@ -1,55 +0,0 @@
- CMakeLists.txt | 8 +++-
- src/CMakeLists.txt | 4 ++--
- 2 files changed, 5 insertions(+), 7 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index c768e28..65d5633 100644
a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)
- set(${PROJECT_NAME}_VERSION_MINOR 5)
- set(${PROJECT_NAME}_VERSION_PATCH 1)
-
--set(CMAKE_CXX_FLAGS "-Wall")
--
- set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}")
- set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}")
- set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}")
-
- set(CMAKE_BUILD_TYPE Release)
--set(Boost_USE_STATIC_LIBS ON)
-+set(Boost_USE_STATIC_LIBS OFF)
-
- find_package(Boost 1.39
- COMPONENTS
-@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB)
-
- find_package(Protobuf)
- if (PROTOBUF_FOUND)
-- include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR}
"${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include")
-+ include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR}
${BAMTOOLS_INCLUDE})
- set(PROTO_INT 1)
- else (PROTOBUF_FOUND)
-- include_directories(${Boost_INCLUDE_DIRS}
"${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include")
-+ include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE})
- set(PROTO_INT 0)
- endif(PROTOBUF_FOUND)
-
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 1cc0c01..8929d1f 100644
a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC)
- if(WIN32)
- set(LIBRARIES ${LIBRARIES}
"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib"
"${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib")
- else(WIN32)
-- set(LIBRARIES
[gentoo-commits] repo/gentoo:master commit in: sci-biology/express/
commit: 4fd2ac9cbf5106e0a2997c99b7c43668128b67ad Author: David Seifert gentoo org> AuthorDate: Sun Sep 4 13:03:25 2022 + Commit: David Seifert gentoo org> CommitDate: Sun Sep 4 13:03:25 2022 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4fd2ac9c sci-biology/express: remove stale boost lower bounds Signed-off-by: David Seifert 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
[gentoo-commits] repo/gentoo:master commit in: sci-biology/express/
commit: f2884a9364159fef2f3dc686ed00ce315088661a
Author: Andreas Sturmlechner gentoo org>
AuthorDate: Sat Mar 6 19:32:53 2021 +
Commit: Andreas Sturmlechner gentoo org>
CommitDate: Sun Mar 7 19:01:10 2021 +
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 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
}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/express/
commit: fad62bd824b9ea69a19200061544567eb9e78730
Author: Andreas Sturmlechner gentoo org>
AuthorDate: Sun Oct 14 16:30:19 2018 +
Commit: Andreas Sturmlechner gentoo org>
CommitDate: Sun Oct 14 16:34:29 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fad62bd8
sci-biology/express: Drop old
Signed-off-by: Andreas Sturmlechner 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..000
--- 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|"${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a"|bamtools|' \
- -e '1 a find_package(Boost 1.52 COMPONENTS filesystem
program_options system thread)' \
- -e '1 a find_package(ZLIB)' \
- -e '/add_executable/ a
include_directories("/usr/include/bamtools")' \
- -i src/CMakeLists.txt || die
-
- cmake-utils_src_prepare
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/express/
commit: 2e39fa5d652b78dfd2d3fb38f2165e6e358dd587
Author: Andreas Sturmlechner gentoo org>
AuthorDate: Sun Oct 14 16:29:31 2018 +
Commit: Andreas Sturmlechner gentoo org>
CommitDate: Sun Oct 14 16:34:29 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2e39fa5d
sci-biology/express: EAPI-6 bump
Signed-off-by: Andreas Sturmlechner gentoo.org>
Package-Manager: Portage-2.3.51, Repoman-2.3.11
sci-biology/express/express-1.5.1.ebuild | 7 ---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/sci-biology/express/express-1.5.1.ebuild
b/sci-biology/express/express-1.5.1.ebuild
index 62e5361f529..148df8a8ce1 100644
--- a/sci-biology/express/express-1.5.1.ebuild
+++ b/sci-biology/express/express-1.5.1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
inherit cmake-utils
@@ -18,8 +18,9 @@ DEPEND="
>=dev-libs/boost-1.52.0:=
dev-libs/protobuf
dev-util/google-perftools
+ sci-biology/bamtools
sys-libs/zlib
- sci-biology/bamtools"
+"
RDEPEND="${DEPEND}"
S="${WORKDIR}/${P}-src"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/express/, sci-biology/express/files/
commit: 61d3ecd7b439ebd0d08613df3dd92b272bb523de
Author: Peter Levine gmail com>
AuthorDate: Sun Jul 23 01:31:58 2017 +
Commit: David Seifert gentoo org>
CommitDate: Sun Jul 30 09:09:27 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61d3ecd7
sci-biology/express: Fix building with GCC-6
Bug: https://bugs.gentoo.org/show_bug.cgi?id=610692
Package-Manager: Portage-2.3.6, Repoman-2.3.2
Closes: https://github.com/gentoo/gentoo/pull/5179
sci-biology/express/express-1.5.1.ebuild | 3 ++-
sci-biology/express/files/express-1.5.1-gcc6.patch | 19 +++
2 files changed, 21 insertions(+), 1 deletion(-)
diff --git a/sci-biology/express/express-1.5.1.ebuild
b/sci-biology/express/express-1.5.1.ebuild
index 5a7ef2f98f0..62e5361f529 100644
--- a/sci-biology/express/express-1.5.1.ebuild
+++ b/sci-biology/express/express-1.5.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -26,6 +26,7 @@ S="${WORKDIR}/${P}-src"
PATCHES=(
"${FILESDIR}"/${P}-buildsystem.patch
+ "${FILESDIR}"/${P}-gcc6.patch
)
src_configure() {
diff --git a/sci-biology/express/files/express-1.5.1-gcc6.patch
b/sci-biology/express/files/express-1.5.1-gcc6.patch
new file mode 100644
index 000..8a608b97b05
--- /dev/null
+++ b/sci-biology/express/files/express-1.5.1-gcc6.patch
@@ -0,0 +1,19 @@
+Bug: https://bugs.gentoo.org/610692
+
+--- a/src/targets.cpp
b/src/targets.cpp
+@@ -113,12 +113,12 @@
+
+ double ll = LOG_1;
+ double tot_mass = mass(with_pseudo);
+- double tot_eff_len = cached_effective_length(lib.bias_table);
++ double tot_eff_len =
cached_effective_length(static_cast(lib.bias_table));
+ if (neighbors) {
+ foreach (const Target* neighbor, *neighbors) {
+ tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo));
+ tot_eff_len = log_add(tot_eff_len,
+-
neighbor->cached_effective_length(lib.bias_table));
++
neighbor->cached_effective_length(static_cast(lib.bias_table)));
+ }
+ }
+ ll += tot_mass - tot_eff_len;
