* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2017-12-23 18:45 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2017-12-23 18:45 UTC (permalink / raw
To: gentoo-commits
commit: a1b05c071c6654e2c96dac44a6b2e599a56a42c7
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 23 18:37:39 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Dec 23 18:45:28 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a1b05c07
sci-biology/bamtools: Add support for static libraries
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/bamtools/bamtools-9999.ebuild | 38 +++++++++++++++++++++++++++++--
1 file changed, 36 insertions(+), 2 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild
index bd0157db0d1..ba21654b97f 100644
--- a/sci-biology/bamtools/bamtools-9999.ebuild
+++ b/sci-biology/bamtools/bamtools-9999.ebuild
@@ -3,7 +3,7 @@
EAPI=6
-inherit cmake-utils
+inherit cmake-utils multibuild
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
HOMEPAGE="https://github.com/pezmaster31/bamtools"
@@ -18,6 +18,7 @@ fi
LICENSE="MIT"
SLOT="0/${PV}" # no stable ABI yet
+IUSE="static-libs"
RDEPEND="
>=dev-libs/jsoncpp-1.8.0:=
@@ -25,7 +26,13 @@ RDEPEND="
DEPEND="${RDEPEND}
virtual/pkgconfig"
-mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] &&
+ MULTIBUILD_VARIANTS=(
+ $(usev static-libs)
+ shared
+ )
+}
src_prepare() {
# delete bundled libs, just to be safe
@@ -33,3 +40,30 @@ src_prepare() {
cmake-utils_src_prepare
}
+
+src_configure() {
+ my_configure() {
+ case "${MULTIBUILD_ID}" in
+ static*)
+ local mycmakeargs=( -DBUILD_SHARED_LIBS=OFF )
+ ;;
+ shared)
+ local mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
+ ;;
+ *)
+ die "${MULTIBUILD_ID} is not recognized"
+ ;;
+ esac
+
+ cmake-utils_src_configure
+ }
+ multibuild_foreach_variant my_configure
+}
+
+src_compile() {
+ multibuild_foreach_variant cmake-utils_src_compile
+}
+
+src_install() {
+ multibuild_foreach_variant cmake-utils_src_install
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2021-06-20 20:04 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2021-06-20 20:04 UTC (permalink / raw
To: gentoo-commits
commit: 76c0d35a1a7694289c8bf7fb3ebc19a159546e86
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 20 20:03:49 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 20 20:03:49 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=76c0d35a
sci-biology/bamtools: add 2.5.2
Bug: https://bugs.gentoo.org/787200
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bamtools/Manifest | 1 +
sci-biology/bamtools/bamtools-2.5.2.ebuild | 33 ++++++++++++++++++++++++++++++
2 files changed, 34 insertions(+)
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index 424c08d5159..e6d9b12cb13 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1 +1,2 @@
DIST bamtools-2.5.1.tar.gz 549750 BLAKE2B c00b42b10e074e2c6b06f8bc9277a57080b9e99cd10080b1ad9052d59a3db353b33ecf6c30642d1651897396ea65e1e19cb15db0d58a89d4375fe34a8ec38e55 SHA512 f2c761c5bf923cf2f3db3dc54e40b4781307106b9177784f930aab619bd11fae3b343f3cfd232524580d39f0526a2a2f18efcf820fe4d9c951406bdb6b953afb
+DIST bamtools-2.5.2.tar.gz 245729 BLAKE2B 5034ea1ec16b205488e421461ed74d8a98eae87eb7fc061e5928ad15512497a5338c9dbacbde51009c940acd55c25fccc2f3be2840d2821a8755a2a0b0370944 SHA512 540a4664abfbd1304600c17d47424c312a46e4238b0f0868f4037ddcc54c4487424e3d7820153084b3b512be8a4603e3ec5377a73311a617061460de1bfe49ef
diff --git a/sci-biology/bamtools/bamtools-2.5.2.ebuild b/sci-biology/bamtools/bamtools-2.5.2.ebuild
new file mode 100644
index 00000000000..a809a651df6
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-2.5.2.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
+else
+ SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0/${PV}" # no stable ABI yet
+
+RDEPEND="
+ >=dev-libs/jsoncpp-1.8.0:=
+ sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+src_prepare() {
+ # delete bundled libs, just to be safe
+ rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
+
+ cmake_src_prepare
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2021-06-20 20:04 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2021-06-20 20:04 UTC (permalink / raw
To: gentoo-commits
commit: 92bb3cbc3bf6874aa00912882ef4fccc0d0c1223
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 20 20:03:52 2021 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 20 20:03:52 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=92bb3cbc
sci-biology/bamtools: drop 2.5.1
Closes: https://bugs.gentoo.org/787200
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bamtools/Manifest | 1 -
sci-biology/bamtools/bamtools-2.5.1.ebuild | 33 ------------------------------
2 files changed, 34 deletions(-)
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index e6d9b12cb13..5076fcaf183 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1,2 +1 @@
-DIST bamtools-2.5.1.tar.gz 549750 BLAKE2B c00b42b10e074e2c6b06f8bc9277a57080b9e99cd10080b1ad9052d59a3db353b33ecf6c30642d1651897396ea65e1e19cb15db0d58a89d4375fe34a8ec38e55 SHA512 f2c761c5bf923cf2f3db3dc54e40b4781307106b9177784f930aab619bd11fae3b343f3cfd232524580d39f0526a2a2f18efcf820fe4d9c951406bdb6b953afb
DIST bamtools-2.5.2.tar.gz 245729 BLAKE2B 5034ea1ec16b205488e421461ed74d8a98eae87eb7fc061e5928ad15512497a5338c9dbacbde51009c940acd55c25fccc2f3be2840d2821a8755a2a0b0370944 SHA512 540a4664abfbd1304600c17d47424c312a46e4238b0f0868f4037ddcc54c4487424e3d7820153084b3b512be8a4603e3ec5377a73311a617061460de1bfe49ef
diff --git a/sci-biology/bamtools/bamtools-2.5.1.ebuild b/sci-biology/bamtools/bamtools-2.5.1.ebuild
deleted file mode 100644
index 78a0c3cd255..00000000000
--- a/sci-biology/bamtools/bamtools-2.5.1.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
-HOMEPAGE="https://github.com/pezmaster31/bamtools"
-
-if [[ ${PV} == *9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
-else
- SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0/${PV}" # no stable ABI yet
-
-RDEPEND="
- >=dev-libs/jsoncpp-1.8.0:=
- sys-libs/zlib:="
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
- # delete bundled libs, just to be safe
- rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
-
- cmake_src_prepare
-}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2020-04-14 8:35 Joonas Niilola
0 siblings, 0 replies; 14+ messages in thread
From: Joonas Niilola @ 2020-04-14 8:35 UTC (permalink / raw
To: gentoo-commits
commit: 7bbdbfd194355a211e18c4ef5f8a7e21cc024ba3
Author: Joonas Niilola <juippis <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 14 07:57:34 2020 +0000
Commit: Joonas Niilola <juippis <AT> gentoo <DOT> org>
CommitDate: Tue Apr 14 08:34:31 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7bbdbfd1
sci-biology/bamtools: remove inactive maintainer
Signed-off-by: Joonas Niilola <juippis <AT> gentoo.org>
sci-biology/bamtools/metadata.xml | 8 --------
1 file changed, 8 deletions(-)
diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml
index f703e6a8289..9aa0cee0cf7 100644
--- a/sci-biology/bamtools/metadata.xml
+++ b/sci-biology/bamtools/metadata.xml
@@ -1,18 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@gmail.com</email>
- <name>Martin Mokrejs</name>
- </maintainer>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
- <maintainer type="project">
- <email>proxy-maint@gentoo.org</email>
- <name>Proxy Maintainers</name>
- </maintainer>
<longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription>
<upstream>
<remote-id type="github">pezmaster31/bamtools</remote-id>
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2019-11-13 18:16 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2019-11-13 18:16 UTC (permalink / raw
To: gentoo-commits
commit: a217ed25f690d9d4ed7b492df1d0d4205830fa3f
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Wed Nov 13 18:16:02 2019 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Wed Nov 13 18:16:02 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a217ed25
sci-biology/bamtools: Remove USE="static-libs"
Package-Manager: Portage-2.3.78, Repoman-2.3.17
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bamtools/bamtools-2.5.1.ebuild | 33 +++---------------------------
sci-biology/bamtools/bamtools-9999.ebuild | 33 +++---------------------------
2 files changed, 6 insertions(+), 60 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-2.5.1.ebuild b/sci-biology/bamtools/bamtools-2.5.1.ebuild
index 84c9dc83723..b5affe9f0fa 100644
--- a/sci-biology/bamtools/bamtools-2.5.1.ebuild
+++ b/sci-biology/bamtools/bamtools-2.5.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit cmake-utils multibuild
+inherit cmake-utils
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
HOMEPAGE="https://github.com/pezmaster31/bamtools"
@@ -18,7 +18,6 @@ fi
LICENSE="MIT"
SLOT="0/${PV}" # no stable ABI yet
-IUSE="static-libs"
RDEPEND="
>=dev-libs/jsoncpp-1.8.0:=
@@ -26,35 +25,9 @@ RDEPEND="
DEPEND="${RDEPEND}"
BDEPEND="virtual/pkgconfig"
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] &&
- MULTIBUILD_VARIANTS=(
- $(usev static-libs)
- shared
- )
-}
-
src_prepare() {
# delete bundled libs, just to be safe
- rm -r src/third_party/{gtest-1.6.0,jsoncpp} || die
+ rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
cmake-utils_src_prepare
}
-
-src_configure() {
- my_configure() {
- [[ ${MULTIBUILD_ID} == static-libs* ]] &&
- local mycmakeargs=( -DBUILD_SHARED_LIBS=OFF )
-
- cmake-utils_src_configure
- }
- multibuild_foreach_variant my_configure
-}
-
-src_compile() {
- multibuild_foreach_variant cmake-utils_src_compile
-}
-
-src_install() {
- multibuild_foreach_variant cmake-utils_src_install
-}
diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild
index 84c9dc83723..b5affe9f0fa 100644
--- a/sci-biology/bamtools/bamtools-9999.ebuild
+++ b/sci-biology/bamtools/bamtools-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit cmake-utils multibuild
+inherit cmake-utils
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
HOMEPAGE="https://github.com/pezmaster31/bamtools"
@@ -18,7 +18,6 @@ fi
LICENSE="MIT"
SLOT="0/${PV}" # no stable ABI yet
-IUSE="static-libs"
RDEPEND="
>=dev-libs/jsoncpp-1.8.0:=
@@ -26,35 +25,9 @@ RDEPEND="
DEPEND="${RDEPEND}"
BDEPEND="virtual/pkgconfig"
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] &&
- MULTIBUILD_VARIANTS=(
- $(usev static-libs)
- shared
- )
-}
-
src_prepare() {
# delete bundled libs, just to be safe
- rm -r src/third_party/{gtest-1.6.0,jsoncpp} || die
+ rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
cmake-utils_src_prepare
}
-
-src_configure() {
- my_configure() {
- [[ ${MULTIBUILD_ID} == static-libs* ]] &&
- local mycmakeargs=( -DBUILD_SHARED_LIBS=OFF )
-
- cmake-utils_src_configure
- }
- multibuild_foreach_variant my_configure
-}
-
-src_compile() {
- multibuild_foreach_variant cmake-utils_src_compile
-}
-
-src_install() {
- multibuild_foreach_variant cmake-utils_src_install
-}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2018-12-13 14:08 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2018-12-13 14:08 UTC (permalink / raw
To: gentoo-commits
commit: e47f0847b07adb2e6d9bb0f3b1bd491c6f3535fa
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 13 14:07:52 2018 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Dec 13 14:07:52 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e47f0847
sci-biology/bamtools: Bump to EAPI 7
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bamtools/bamtools-2.5.1.ebuild | 22 ++++++----------------
sci-biology/bamtools/bamtools-9999.ebuild | 22 ++++++----------------
2 files changed, 12 insertions(+), 32 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-2.5.1.ebuild b/sci-biology/bamtools/bamtools-2.5.1.ebuild
index 038ed14beb0..84c9dc83723 100644
--- a/sci-biology/bamtools/bamtools-2.5.1.ebuild
+++ b/sci-biology/bamtools/bamtools-2.5.1.ebuild
@@ -1,9 +1,8 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
inherit cmake-utils multibuild
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
@@ -24,8 +23,8 @@ IUSE="static-libs"
RDEPEND="
>=dev-libs/jsoncpp-1.8.0:=
sys-libs/zlib:="
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
pkg_setup() {
[[ ${MERGE_TYPE} != binary ]] &&
@@ -44,17 +43,8 @@ src_prepare() {
src_configure() {
my_configure() {
- case "${MULTIBUILD_ID}" in
- static*)
- local mycmakeargs=( -DBUILD_SHARED_LIBS=OFF )
- ;;
- shared)
- local mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
- ;;
- *)
- die "${MULTIBUILD_ID} is not recognized"
- ;;
- esac
+ [[ ${MULTIBUILD_ID} == static-libs* ]] &&
+ local mycmakeargs=( -DBUILD_SHARED_LIBS=OFF )
cmake-utils_src_configure
}
diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild
index 038ed14beb0..84c9dc83723 100644
--- a/sci-biology/bamtools/bamtools-9999.ebuild
+++ b/sci-biology/bamtools/bamtools-9999.ebuild
@@ -1,9 +1,8 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
inherit cmake-utils multibuild
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
@@ -24,8 +23,8 @@ IUSE="static-libs"
RDEPEND="
>=dev-libs/jsoncpp-1.8.0:=
sys-libs/zlib:="
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
pkg_setup() {
[[ ${MERGE_TYPE} != binary ]] &&
@@ -44,17 +43,8 @@ src_prepare() {
src_configure() {
my_configure() {
- case "${MULTIBUILD_ID}" in
- static*)
- local mycmakeargs=( -DBUILD_SHARED_LIBS=OFF )
- ;;
- shared)
- local mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
- ;;
- *)
- die "${MULTIBUILD_ID} is not recognized"
- ;;
- esac
+ [[ ${MULTIBUILD_ID} == static-libs* ]] &&
+ local mycmakeargs=( -DBUILD_SHARED_LIBS=OFF )
cmake-utils_src_configure
}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2018-06-02 13:25 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2018-06-02 13:25 UTC (permalink / raw
To: gentoo-commits
commit: 72c315a37ce2ecc654db481686b75c7952d4dd2d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 2 10:58:59 2018 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jun 2 13:24:55 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=72c315a3
sci-biology/bamtools: Use ninja for building
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/bamtools/bamtools-2.5.1.ebuild | 3 ++-
sci-biology/bamtools/bamtools-9999.ebuild | 3 ++-
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-2.5.1.ebuild b/sci-biology/bamtools/bamtools-2.5.1.ebuild
index ba21654b97f..038ed14beb0 100644
--- a/sci-biology/bamtools/bamtools-2.5.1.ebuild
+++ b/sci-biology/bamtools/bamtools-2.5.1.ebuild
@@ -1,8 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
+: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
inherit cmake-utils multibuild
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild
index ba21654b97f..038ed14beb0 100644
--- a/sci-biology/bamtools/bamtools-9999.ebuild
+++ b/sci-biology/bamtools/bamtools-9999.ebuild
@@ -1,8 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
+: ${CMAKE_MAKEFILE_GENERATOR:=ninja}
inherit cmake-utils multibuild
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2017-12-23 18:45 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2017-12-23 18:45 UTC (permalink / raw
To: gentoo-commits
commit: 483f71801c8c59240ed81cb1e7bc5e3aad9a2a19
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 23 18:44:56 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Dec 23 18:45:40 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=483f7180
sci-biology/bamtools: Remove old
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/bamtools/Manifest | 1 -
sci-biology/bamtools/bamtools-2.4.2.ebuild | 35 ------------------------------
2 files changed, 36 deletions(-)
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index da707d0eb8f..424c08d5159 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1,2 +1 @@
-DIST bamtools-2.4.2.tar.gz 548095 BLAKE2B 19f302eb5de9c8e3f0dc53cb9cbb359b1186b44318f7cb82e83ea995920bb30331d0873c9ad9c68601306772eab1283ead2b0eb4a8cb17cb1eade600c9cdbfac SHA512 244a63609c0b10a85bba7cac210a27ea9abafba136e9c91fc789c7aa21a6cdaa7622afebc50ec8d30d4446872d5206dbd3d679ca03e95ac90771c87359cb69a0
DIST bamtools-2.5.1.tar.gz 549750 BLAKE2B c00b42b10e074e2c6b06f8bc9277a57080b9e99cd10080b1ad9052d59a3db353b33ecf6c30642d1651897396ea65e1e19cb15db0d58a89d4375fe34a8ec38e55 SHA512 f2c761c5bf923cf2f3db3dc54e40b4781307106b9177784f930aab619bd11fae3b343f3cfd232524580d39f0526a2a2f18efcf820fe4d9c951406bdb6b953afb
diff --git a/sci-biology/bamtools/bamtools-2.4.2.ebuild b/sci-biology/bamtools/bamtools-2.4.2.ebuild
deleted file mode 100644
index bd0157db0d1..00000000000
--- a/sci-biology/bamtools/bamtools-2.4.2.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
-HOMEPAGE="https://github.com/pezmaster31/bamtools"
-
-if [[ ${PV} == *9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
-else
- SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="MIT"
-SLOT="0/${PV}" # no stable ABI yet
-
-RDEPEND="
- >=dev-libs/jsoncpp-1.8.0:=
- sys-libs/zlib:="
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
-
-src_prepare() {
- # delete bundled libs, just to be safe
- rm -r src/third_party/{gtest-1.6.0,jsoncpp} || die
-
- cmake-utils_src_prepare
-}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2017-12-23 18:45 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2017-12-23 18:45 UTC (permalink / raw
To: gentoo-commits
commit: a4fea019175a1a73486a1f759b0cafc875826072
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 23 18:44:09 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Dec 23 18:45:34 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a4fea019
sci-biology/bamtools: Version bump to 2.5.1
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/bamtools/Manifest | 1 +
sci-biology/bamtools/bamtools-2.5.1.ebuild | 69 ++++++++++++++++++++++++++++++
2 files changed, 70 insertions(+)
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index bd3643e1a9e..da707d0eb8f 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1 +1,2 @@
DIST bamtools-2.4.2.tar.gz 548095 BLAKE2B 19f302eb5de9c8e3f0dc53cb9cbb359b1186b44318f7cb82e83ea995920bb30331d0873c9ad9c68601306772eab1283ead2b0eb4a8cb17cb1eade600c9cdbfac SHA512 244a63609c0b10a85bba7cac210a27ea9abafba136e9c91fc789c7aa21a6cdaa7622afebc50ec8d30d4446872d5206dbd3d679ca03e95ac90771c87359cb69a0
+DIST bamtools-2.5.1.tar.gz 549750 BLAKE2B c00b42b10e074e2c6b06f8bc9277a57080b9e99cd10080b1ad9052d59a3db353b33ecf6c30642d1651897396ea65e1e19cb15db0d58a89d4375fe34a8ec38e55 SHA512 f2c761c5bf923cf2f3db3dc54e40b4781307106b9177784f930aab619bd11fae3b343f3cfd232524580d39f0526a2a2f18efcf820fe4d9c951406bdb6b953afb
diff --git a/sci-biology/bamtools/bamtools-2.5.1.ebuild b/sci-biology/bamtools/bamtools-2.5.1.ebuild
new file mode 100644
index 00000000000..ba21654b97f
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-2.5.1.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils multibuild
+
+DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
+else
+ SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0/${PV}" # no stable ABI yet
+IUSE="static-libs"
+
+RDEPEND="
+ >=dev-libs/jsoncpp-1.8.0:=
+ sys-libs/zlib:="
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
+
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] &&
+ MULTIBUILD_VARIANTS=(
+ $(usev static-libs)
+ shared
+ )
+}
+
+src_prepare() {
+ # delete bundled libs, just to be safe
+ rm -r src/third_party/{gtest-1.6.0,jsoncpp} || die
+
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ my_configure() {
+ case "${MULTIBUILD_ID}" in
+ static*)
+ local mycmakeargs=( -DBUILD_SHARED_LIBS=OFF )
+ ;;
+ shared)
+ local mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
+ ;;
+ *)
+ die "${MULTIBUILD_ID} is not recognized"
+ ;;
+ esac
+
+ cmake-utils_src_configure
+ }
+ multibuild_foreach_variant my_configure
+}
+
+src_compile() {
+ multibuild_foreach_variant cmake-utils_src_compile
+}
+
+src_install() {
+ multibuild_foreach_variant cmake-utils_src_install
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2017-11-02 3:31 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2017-11-02 3:31 UTC (permalink / raw
To: gentoo-commits
commit: f271f6acc55e7d323a78cc9527507834b8bcedea
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 2 03:30:46 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Nov 2 03:30:46 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f271f6ac
sci-biology/bamtools: Minor fixes
* Add 'virtual/pkgconfig' to DEPEND
* Delete bundled libs for safety
Package-Manager: Portage-2.3.11, Repoman-2.3.3
sci-biology/bamtools/bamtools-2.4.2.ebuild | 10 +++++++++-
sci-biology/bamtools/bamtools-9999.ebuild | 10 +++++++++-
2 files changed, 18 insertions(+), 2 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-2.4.2.ebuild b/sci-biology/bamtools/bamtools-2.4.2.ebuild
index e6daa826202..bd0157db0d1 100644
--- a/sci-biology/bamtools/bamtools-2.4.2.ebuild
+++ b/sci-biology/bamtools/bamtools-2.4.2.ebuild
@@ -22,6 +22,14 @@ SLOT="0/${PV}" # no stable ABI yet
RDEPEND="
>=dev-libs/jsoncpp-1.8.0:=
sys-libs/zlib:="
-DEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
+
+src_prepare() {
+ # delete bundled libs, just to be safe
+ rm -r src/third_party/{gtest-1.6.0,jsoncpp} || die
+
+ cmake-utils_src_prepare
+}
diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild
index e6daa826202..bd0157db0d1 100644
--- a/sci-biology/bamtools/bamtools-9999.ebuild
+++ b/sci-biology/bamtools/bamtools-9999.ebuild
@@ -22,6 +22,14 @@ SLOT="0/${PV}" # no stable ABI yet
RDEPEND="
>=dev-libs/jsoncpp-1.8.0:=
sys-libs/zlib:="
-DEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig"
mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
+
+src_prepare() {
+ # delete bundled libs, just to be safe
+ rm -r src/third_party/{gtest-1.6.0,jsoncpp} || die
+
+ cmake-utils_src_prepare
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2017-11-02 3:19 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2017-11-02 3:19 UTC (permalink / raw
To: gentoo-commits
commit: f84da63476bd6108105d349f74e6710237a8b290
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 2 03:19:34 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Nov 2 03:19:34 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f84da634
sci-biology/bamtools: Version bump to 2.4.2
Package-Manager: Portage-2.3.11, Repoman-2.3.3
sci-biology/bamtools/Manifest | 1 +
sci-biology/bamtools/bamtools-2.4.2.ebuild | 27 +++++++++++++++++++++++++++
2 files changed, 28 insertions(+)
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index f276fed1152..45492cd4dca 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1 +1,2 @@
DIST bamtools-2.4.1.tar.gz 540482 SHA256 933a0c1a83c88c1dac8078c0c0e82f6794c75cb927265399404bc2cc2611204b SHA512 ee674014f27b2dc0aa7c0415e8654ee7c39cfdecafbd9983d970fad6ad29f070a7ff372ee05765956cf7c8f8bb3b9763b6e537e693a0d2d64680148b1a23cfee WHIRLPOOL 6ef73f0713ebf993123eac7095061e32fe6a53db383e28a5dd8967afee92fb211ce56611de9718ce4cce84bdee14157ff968e0a6edcaead4e06b44008b78b84c
+DIST bamtools-2.4.2.tar.gz 548095 SHA256 04165bf8a7566f4be1a6e68f69bfdd9f08364ba7b0d2f6687302434641408102 SHA512 244a63609c0b10a85bba7cac210a27ea9abafba136e9c91fc789c7aa21a6cdaa7622afebc50ec8d30d4446872d5206dbd3d679ca03e95ac90771c87359cb69a0 WHIRLPOOL e1ed40d1ec47cbe97c4de160671f34095bf56f5786ebcc0cf7fb7b5e4b129d9c562b1cf19fb1d22e3ef20fa21d45f1fe50640b9d9919c01fabed044f82c9c2de
diff --git a/sci-biology/bamtools/bamtools-2.4.2.ebuild b/sci-biology/bamtools/bamtools-2.4.2.ebuild
new file mode 100644
index 00000000000..e6daa826202
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-2.4.2.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils
+
+DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
+else
+ SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0/${PV}" # no stable ABI yet
+
+RDEPEND="
+ >=dev-libs/jsoncpp-1.8.0:=
+ sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+
+mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2017-11-02 3:19 David Seifert
0 siblings, 0 replies; 14+ messages in thread
From: David Seifert @ 2017-11-02 3:19 UTC (permalink / raw
To: gentoo-commits
commit: 79838b33f1601376b91619946571004aa16be3a1
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 2 03:19:37 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Nov 2 03:19:37 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=79838b33
sci-biology/bamtools: Add live ebuild
Package-Manager: Portage-2.3.11, Repoman-2.3.3
sci-biology/bamtools/bamtools-9999.ebuild | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild
new file mode 100644
index 00000000000..e6daa826202
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-9999.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils
+
+DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
+else
+ SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0/${PV}" # no stable ABI yet
+
+RDEPEND="
+ >=dev-libs/jsoncpp-1.8.0:=
+ sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+
+mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2015-12-13 9:54 Justin Lecher
0 siblings, 0 replies; 14+ messages in thread
From: Justin Lecher @ 2015-12-13 9:54 UTC (permalink / raw
To: gentoo-commits
commit: 8deb276adb49578cf19bce5ef8fe9394aa90db6f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 13 09:19:12 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Dec 13 09:19:12 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8deb276a
sci-biology/bamtools: Unbundle dev-libs/jsoncpp
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=568090
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
...tools-1.0.2.ebuild => bamtools-1.0.2-r1.ebuild} | 33 ++++++++++++++++------
1 file changed, 24 insertions(+), 9 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-1.0.2.ebuild b/sci-biology/bamtools/bamtools-1.0.2-r1.ebuild
similarity index 53%
rename from sci-biology/bamtools/bamtools-1.0.2.ebuild
rename to sci-biology/bamtools/bamtools-1.0.2-r1.ebuild
index 08c40d0..dc1b60b 100644
--- a/sci-biology/bamtools/bamtools-1.0.2.ebuild
+++ b/sci-biology/bamtools/bamtools-1.0.2-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=4
+EAPI=5
inherit cmake-utils
@@ -15,19 +15,34 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND="sys-libs/zlib"
-RDEPEND="${DEPEND}"
+RDEPEND="
+ dev-libs/jsoncpp
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ sed \
+ -e '/third_party/d' \
+ -i src/CMakeLists.txt || die
+ rm -r src/third_party || die
+
+ sed \
+ -e 's:json.h:json/json.h:g' \
+ -i src/toolkit/bamtools_filter.cpp || die
+
+ cmake-utils_src_prepare
+}
src_install() {
+ local i
for i in bin/bamtools-${PV} lib/libbamtools.so.${PV} lib/libbamtools-utils.so.${PV}; do
TMPDIR="$(pwd)" scanelf -Xr $i || die
done
dobin bin/bamtools
- dolib lib/*
- insinto /usr/include/bamtools/api
- doins include/api/*
- insinto /usr/include/bamtools/shared
- doins include/shared/*
+ dolib.so lib/*so*
+ use static-libs && dolib.a lib/*a
+ insinto /usr/include/bamtools
+ doins include/api include/shared
dodoc README
}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
@ 2015-08-16 11:30 Justin Lecher
0 siblings, 0 replies; 14+ messages in thread
From: Justin Lecher @ 2015-08-16 11:30 UTC (permalink / raw
To: gentoo-commits
commit: 8c05129e3e2fce50f23c7c5c6015575f686f6e8f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 16 11:18:23 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Aug 16 11:30:22 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8c05129e
sci-biology/bamtools: Restrict Version of dev-libs/jsoncpp in deps, bug #550144 https://github.com/pezmaster31/bamtools/issues/108
Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/bamtools/bamtools-2.3.0.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bamtools/bamtools-2.3.0.ebuild b/sci-biology/bamtools/bamtools-2.3.0.ebuild
index cb86750..5b6468c 100644
--- a/sci-biology/bamtools/bamtools-2.3.0.ebuild
+++ b/sci-biology/bamtools/bamtools-2.3.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,6 +17,7 @@ IUSE="static-libs"
DEPEND="
>=dev-libs/jsoncpp-0.5.0-r1
+ <dev-libs/jsoncpp-1
sys-libs/zlib"
RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 14+ messages in thread
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