[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: 92bb3cbc3bf6874aa00912882ef4fccc0d0c1223
Author: David Seifert gentoo org>
AuthorDate: Sun Jun 20 20:03:52 2021 +
Commit: David Seifert gentoo org>
CommitDate: Sun Jun 20 20:03:52 2021 +
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 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..000
--- 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 [[ ${PV} == * ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git;
-else
- SRC_URI="https://github.com/pezmaster31/${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
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: 76c0d35a1a7694289c8bf7fb3ebc19a159546e86
Author: David Seifert gentoo org>
AuthorDate: Sun Jun 20 20:03:49 2021 +
Commit: David Seifert gentoo org>
CommitDate: Sun Jun 20 20:03:49 2021 +
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 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 000..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 [[ ${PV} == * ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git;
+else
+ SRC_URI="https://github.com/pezmaster31/${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
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: 7bbdbfd194355a211e18c4ef5f8a7e21cc024ba3 Author: Joonas Niilola gentoo org> AuthorDate: Tue Apr 14 07:57:34 2020 + Commit: Joonas Niilola gentoo org> CommitDate: Tue Apr 14 08:34:31 2020 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7bbdbfd1 sci-biology/bamtools: remove inactive maintainer Signed-off-by: Joonas Niilola 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 @@ http://www.gentoo.org/dtd/metadata.dtd;> - -mmokr...@gmail.com -Martin Mokrejs - sci-biol...@gentoo.org Gentoo Biology Project - -proxy-ma...@gentoo.org -Proxy Maintainers - 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. pezmaster31/bamtools
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/, sci-libs/dcmtk/, sci-libs/symengine/
commit: 4ffa10f6a70318d6b036be816b8da47711eeebb7
Author: Andreas Sturmlechner gentoo org>
AuthorDate: Sat Jan 4 10:14:15 2020 +
Commit: Andreas Sturmlechner gentoo org>
CommitDate: Sun Jan 5 17:40:24 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4ffa10f6
*/*: Switch sci-biology proj to cmake.eclass
Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Andreas Sturmlechner gentoo.org>
sci-biology/bamtools/bamtools-2.5.1.ebuild | 6 +++---
sci-biology/bamtools/bamtools-.ebuild | 6 +++---
sci-libs/dcmtk/dcmtk-3.6.5.ebuild | 11 +--
sci-libs/symengine/symengine-0.5.0.ebuild | 8
4 files changed, 15 insertions(+), 16 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-2.5.1.ebuild
b/sci-biology/bamtools/bamtools-2.5.1.ebuild
index b5affe9f0fa..78a0c3cd255 100644
--- a/sci-biology/bamtools/bamtools-2.5.1.ebuild
+++ b/sci-biology/bamtools/bamtools-2.5.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit cmake-utils
+inherit cmake
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM
files"
HOMEPAGE="https://github.com/pezmaster31/bamtools;
@@ -29,5 +29,5 @@ src_prepare() {
# delete bundled libs, just to be safe
rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
- cmake-utils_src_prepare
+ cmake_src_prepare
}
diff --git a/sci-biology/bamtools/bamtools-.ebuild
b/sci-biology/bamtools/bamtools-.ebuild
index b5affe9f0fa..78a0c3cd255 100644
--- a/sci-biology/bamtools/bamtools-.ebuild
+++ b/sci-biology/bamtools/bamtools-.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit cmake-utils
+inherit cmake
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM
files"
HOMEPAGE="https://github.com/pezmaster31/bamtools;
@@ -29,5 +29,5 @@ src_prepare() {
# delete bundled libs, just to be safe
rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
- cmake-utils_src_prepare
+ cmake_src_prepare
}
diff --git a/sci-libs/dcmtk/dcmtk-3.6.5.ebuild
b/sci-libs/dcmtk/dcmtk-3.6.5.ebuild
index 62dcaa4d598..240ca02f96f 100644
--- a/sci-libs/dcmtk/dcmtk-3.6.5.ebuild
+++ b/sci-libs/dcmtk/dcmtk-3.6.5.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit cmake-utils
+inherit cmake
DESCRIPTION="The DICOM Toolkit"
HOMEPAGE="https://dicom.offis.de/dcmtk.php.en;
@@ -30,7 +30,7 @@ DEPEND="${RDEPEND}
BDEPEND="doc? ( app-doc/doxygen )"
src_prepare() {
- cmake-utils_src_prepare
+ cmake_src_prepare
sed -e "s:share/doc/dcmtk:&-${PV}:" \
-e "s:DIR \"/:DIR \"/usr/:" \
@@ -51,7 +51,6 @@ src_prepare() {
src_configure() {
local mycmakeargs=(
- -DBUILD_SHARED_LIBS=ON
-DCMAKE_INSTALL_SYSCONFDIR="${EROOT}/etc"
-DDCMTK_WITH_ICU=ON
-DDCMTK_WITH_TIFF=$(usex tiff)
@@ -63,7 +62,7 @@ src_configure() {
-DDCMTK_WITH_THREADS=$(usex threads)
)
- cmake-utils_src_configure
+ cmake_src_configure
if use doc; then
cd "${S}"/doxygen || die
@@ -72,7 +71,7 @@ src_configure() {
}
src_compile() {
- cmake-utils_src_compile
+ cmake_src_compile
if use doc; then
emake -C "${S}"/doxygen
@@ -85,5 +84,5 @@ src_install() {
if use doc; then
local HTML_DOCS=( "${S}"/doxygen/htmldocs/. )
fi
- cmake-utils_src_install
+ cmake_src_install
}
diff --git a/sci-libs/symengine/symengine-0.5.0.ebuild
b/sci-libs/symengine/symengine-0.5.0.ebuild
index 725e60e3d7f..6b84f4677d6 100644
--- a/sci-libs/symengine/symengine-0.5.0.ebuild
+++ b/sci-libs/symengine/symengine-0.5.0.ebuild
@@ -3,7 +3,8 @@
EAPI=7
-inherit cmake-utils flag-o-matic
+CMAKE_BUILD_TYPE=Release
+inherit cmake flag-o-matic
DESCRIPTION="Fast symbolic manipulation library, written in C++"
HOMEPAGE="https://github.com/sympy/symengine;
@@ -33,7 +34,7 @@ pkg_pretend() {
}
src_prepare() {
- cmake-utils_src_prepare
+ cmake_src_prepare
sed -e "s|DESTINATION doc| DESTINATION share/doc/${PF}/html|" \
-e "s|/lib|/$(get_libdir)|g" \
-e "s|lib/|$(get_libdir)/|g" \
@@ -57,7 +58,6 @@ src_configure() {
local mycmakeargs=(
-DARB_INCLUDE_DIR="${EPREFIX}/usr/include"
-DINTEGER_CLASS="${int_class}"
- -DBUILD_SHARED_LIBS=ON
-DBUILD_BENCHMARKS="$(usex benchmarks)"
-DBUILD_DOXYGEN="$(usex doc)"
-DBUILD_TESTS="$(usex test)"
@@ -75,5 +75,5 @@ src_configure() {
-DWITH_ECM="$(usex ecm)"
)
test-flag-CXX -std=c++11 &&
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: a217ed25f690d9d4ed7b492df1d0d4205830fa3f
Author: David Seifert gentoo org>
AuthorDate: Wed Nov 13 18:16:02 2019 +
Commit: David Seifert gentoo org>
CommitDate: Wed Nov 13 18:16:02 2019 +
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 gentoo.org>
sci-biology/bamtools/bamtools-2.5.1.ebuild | 33 +++---
sci-biology/bamtools/bamtools-.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() {
- [[ ${MULTIBUILD_ID} == static-libs* ]] &&
- local mycmakeargs=( -DBUILD_SHARED_LIBS=OFF )
-
- cmake-utils_src_configure
- }
- multibuild_foreach_variant my_configure
-}
-
-src_compile() {
- multibuild_foreach_variant cmake-utils_src_compile
-}
-
-src_install() {
- multibuild_foreach_variant cmake-utils_src_install
-}
diff --git a/sci-biology/bamtools/bamtools-.ebuild
b/sci-biology/bamtools/bamtools-.ebuild
index 84c9dc83723..b5affe9f0fa 100644
--- a/sci-biology/bamtools/bamtools-.ebuild
+++ b/sci-biology/bamtools/bamtools-.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit cmake-utils multibuild
+inherit cmake-utils
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM
files"
HOMEPAGE="https://github.com/pezmaster31/bamtools;
@@ -18,7 +18,6 @@ fi
LICENSE="MIT"
SLOT="0/${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
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: e47f0847b07adb2e6d9bb0f3b1bd491c6f3535fa
Author: David Seifert gentoo org>
AuthorDate: Thu Dec 13 14:07:52 2018 +
Commit: David Seifert gentoo org>
CommitDate: Thu Dec 13 14:07:52 2018 +
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 gentoo.org>
sci-biology/bamtools/bamtools-2.5.1.ebuild | 22 ++
sci-biology/bamtools/bamtools-.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-.ebuild
b/sci-biology/bamtools/bamtools-.ebuild
index 038ed14beb0..84c9dc83723 100644
--- a/sci-biology/bamtools/bamtools-.ebuild
+++ b/sci-biology/bamtools/bamtools-.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
}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: 72c315a37ce2ecc654db481686b75c7952d4dd2d
Author: David Seifert gentoo org>
AuthorDate: Sat Jun 2 10:58:59 2018 +
Commit: David Seifert gentoo org>
CommitDate: Sat Jun 2 13:24:55 2018 +
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-.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-.ebuild
b/sci-biology/bamtools/bamtools-.ebuild
index ba21654b97f..038ed14beb0 100644
--- a/sci-biology/bamtools/bamtools-.ebuild
+++ b/sci-biology/bamtools/bamtools-.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"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: a4fea019175a1a73486a1f759b0cafc875826072
Author: David Seifert gentoo org>
AuthorDate: Sat Dec 23 18:44:09 2017 +
Commit: David Seifert gentoo org>
CommitDate: Sat Dec 23 18:45:34 2017 +
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 000..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 [[ ${PV} == * ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git;
+else
+ SRC_URI="https://github.com/pezmaster31/${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 "${MULTIBUILD_ID} is not recognized"
+ ;;
+ esac
+
+ cmake-utils_src_configure
+ }
+ multibuild_foreach_variant my_configure
+}
+
+src_compile() {
+ multibuild_foreach_variant cmake-utils_src_compile
+}
+
+src_install() {
+ multibuild_foreach_variant cmake-utils_src_install
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: a1b05c071c6654e2c96dac44a6b2e599a56a42c7
Author: David Seifert gentoo org>
AuthorDate: Sat Dec 23 18:37:39 2017 +
Commit: David Seifert gentoo org>
CommitDate: Sat Dec 23 18:45:28 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a1b05c07
sci-biology/bamtools: Add support for static libraries
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/bamtools/bamtools-.ebuild | 38 +--
1 file changed, 36 insertions(+), 2 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-.ebuild
b/sci-biology/bamtools/bamtools-.ebuild
index bd0157db0d1..ba21654b97f 100644
--- a/sci-biology/bamtools/bamtools-.ebuild
+++ b/sci-biology/bamtools/bamtools-.ebuild
@@ -3,7 +3,7 @@
EAPI=6
-inherit cmake-utils
+inherit cmake-utils multibuild
DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM
files"
HOMEPAGE="https://github.com/pezmaster31/bamtools;
@@ -18,6 +18,7 @@ fi
LICENSE="MIT"
SLOT="0/${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
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: 483f71801c8c59240ed81cb1e7bc5e3aad9a2a19
Author: David Seifert gentoo org>
AuthorDate: Sat Dec 23 18:44:56 2017 +
Commit: David Seifert gentoo org>
CommitDate: Sat Dec 23 18:45:40 2017 +
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..000
--- 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 [[ ${PV} == * ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git;
-else
- SRC_URI="https://github.com/pezmaster31/${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="${RDEPEND}
- virtual/pkgconfig"
-
-mycmakeargs=( -DBUILD_SHARED_LIBS=ON )
-
-src_prepare() {
- # delete bundled libs, just to be safe
- rm -r src/third_party/{gtest-1.6.0,jsoncpp} || die
-
- cmake-utils_src_prepare
-}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: f271f6acc55e7d323a78cc9527507834b8bcedea
Author: David Seifert gentoo org>
AuthorDate: Thu Nov 2 03:30:46 2017 +
Commit: David Seifert gentoo org>
CommitDate: Thu Nov 2 03:30:46 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f271f6ac
sci-biology/bamtools: Minor fixes
* Add 'virtual/pkgconfig' to DEPEND
* Delete bundled libs for safety
Package-Manager: Portage-2.3.11, Repoman-2.3.3
sci-biology/bamtools/bamtools-2.4.2.ebuild | 10 +-
sci-biology/bamtools/bamtools-.ebuild | 10 +-
2 files changed, 18 insertions(+), 2 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-2.4.2.ebuild
b/sci-biology/bamtools/bamtools-2.4.2.ebuild
index e6daa826202..bd0157db0d1 100644
--- a/sci-biology/bamtools/bamtools-2.4.2.ebuild
+++ b/sci-biology/bamtools/bamtools-2.4.2.ebuild
@@ -22,6 +22,14 @@ SLOT="0/${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-.ebuild
b/sci-biology/bamtools/bamtools-.ebuild
index e6daa826202..bd0157db0d1 100644
--- a/sci-biology/bamtools/bamtools-.ebuild
+++ b/sci-biology/bamtools/bamtools-.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
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: f84da63476bd6108105d349f74e6710237a8b290
Author: David Seifert gentoo org>
AuthorDate: Thu Nov 2 03:19:34 2017 +
Commit: David Seifert gentoo org>
CommitDate: Thu Nov 2 03:19:34 2017 +
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 000..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 [[ ${PV} == * ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git;
+else
+ SRC_URI="https://github.com/pezmaster31/${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 )
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/files/, sci-biology/bamtools/
commit: 70aa79d9e30fc3338314000c13b71ab66bf8552b
Author: David Seifert gentoo org>
AuthorDate: Thu Nov 2 03:19:41 2017 +
Commit: David Seifert gentoo org>
CommitDate: Thu Nov 2 03:19:41 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=70aa79d9
sci-biology/bamtools: Remove old
Package-Manager: Portage-2.3.11, Repoman-2.3.3
sci-biology/bamtools/Manifest | 1 -
sci-biology/bamtools/bamtools-2.4.1.ebuild | 25 ---
.../files/bamtools-2.4.1-fix-build-system.patch| 209 -
.../bamtools/files/bamtools-2.4.1-fix-c++14.patch | 78
4 files changed, 313 deletions(-)
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index 45492cd4dca..855871fa7e3 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1,2 +1 @@
-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-2.4.1.ebuild
b/sci-biology/bamtools/bamtools-2.4.1.ebuild
deleted file mode 100644
index 2196c66790d..000
--- a/sci-biology/bamtools/bamtools-2.4.1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2016 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;
-SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz ->
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- >=dev-libs/jsoncpp-1.8.0
- sys-libs/zlib"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-2.4.1-fix-build-system.patch
- "${FILESDIR}"/${PN}-2.4.1-fix-c++14.patch
-)
diff --git a/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch
b/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch
deleted file mode 100644
index 79597233030..000
--- a/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch
+++ /dev/null
@@ -1,209 +0,0 @@
-* Unbundle jsoncpp
-* Remove forcing C++98
-* Remove forcing CMAKE_BUILD_TYPE
-* Remove -fPIC globally
-* Fix LFS macro definitions
-* Make building static library optional
-* Use GNUInstallDirs conventions
-* Install .pc file
-See also: https://bugs.gentoo.org/show_bug.cgi?id=550144
-
-Taken from https://github.com/pezmaster31/bamtools/pull/139
-
a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -9,7 +9,14 @@
- project( BamTools )
-
- # Cmake requirements
--cmake_minimum_required( VERSION 2.6.4 )
-+cmake_minimum_required( VERSION 3.0 )
-+
-+# on macOS, MACOSX_RPATH is enabled by default on more recent versions
-+# of CMake. Disable this behaviour, and let user enable it if need be.
-+cmake_policy( SET CMP0042 OLD )
-+
-+# Adhere to GNU filesystem layout conventions
-+include( GNUInstallDirs )
-
- # Force the build directory to be different from source directory
- macro( ENSURE_OUT_OF_SOURCE_BUILD MSG )
-@@ -34,18 +41,21 @@
- set( BamTools_VERSION_MINOR 4 )
- set( BamTools_VERSION_BUILD 1 )
-
--# set our library and executable destination dirs
--set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )
--set( LIBRARY_OUTPUT_PATH"${CMAKE_SOURCE_DIR}/lib" )
--
- # define compiler flags for all code
--set( CMAKE_BUILD_TYPE Release )
--set( CMAKE_CXX_FLAGS_RELEASE "-std=c++98 ${CMAKE_CXX_FLAGS_RELEASE}" )
--add_definitions( -Wall -D_FILE_OFFSET_BITS=64 )
-+add_definitions( -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-D_LARGEFILE64_SOURCE )
-+add_compile_options( -Wall )
-
- # ---
- # handle platform-/environment-specific defines
-
-+# Make building the static library optional
-+option( BUILD_STATIC "Build static libbamtools archive" OFF )
-+if( BUILD_STATIC )
-+set( BAMTOOLS_CMD_LDFLAGS BamTools-static )
-+else()
-+set( BAMTOOLS_CMD_LDFLAGS BamTools )
-+endif()
-+
- # If planning to run in Node.js environment, run:
- # cmake -DEnableNodeJS=true
- if( EnableNodeJS )
-@@ -57,6 +67,11 @@
- add_definitions( -DSUN_OS )
- endif()
-
-+# find system JsonCpp
-+find_package( PkgConfig )
-+pkg_search_module( JSONCPP jsoncpp>=1 )
-+
-+
- #
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: 79838b33f1601376b91619946571004aa16be3a1
Author: David Seifert gentoo org>
AuthorDate: Thu Nov 2 03:19:37 2017 +
Commit: David Seifert gentoo org>
CommitDate: Thu Nov 2 03:19:37 2017 +
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-.ebuild | 27 +++
1 file changed, 27 insertions(+)
diff --git a/sci-biology/bamtools/bamtools-.ebuild
b/sci-biology/bamtools/bamtools-.ebuild
new file mode 100644
index 000..e6daa826202
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-.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 [[ ${PV} == * ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git;
+else
+ SRC_URI="https://github.com/pezmaster31/${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 )
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/, sci-biology/bamtools/files/
commit: d7a2a3ae8f4c468241ac6597f1bea2273b154a53
Author: David Seifert gentoo org>
AuthorDate: Wed Dec 14 22:50:25 2016 +
Commit: David Seifert gentoo org>
CommitDate: Thu Dec 15 08:02:19 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d7a2a3ae
sci-biology/bamtools: Remove old
Package-Manager: portage-2.3.3
Closes: https://github.com/gentoo/gentoo/pull/3120
sci-biology/bamtools/Manifest | 2 -
sci-biology/bamtools/bamtools-1.0.2-r1.ebuild | 48 --
sci-biology/bamtools/bamtools-2.3.0.ebuild | 31 --
.../bamtools/files/bamtools-2.3.0-unbundle.patch | 23 ---
4 files changed, 104 deletions(-)
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index fa04b1b..f276fed 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1,3 +1 @@
-DIST bamtools-1.0.2.tar.gz 207523 SHA256
d3ca75d2bec531f15dbc400a76afbe48d47452ce05552c88943bbce81a0862d8 SHA512
1934d40d50f3fdf2b1fcacb8b59cf954a3c791d3095649ac4f1246563e9d8d4afe385e42a2c6c383f0bb519eede401d12c71203d279b33e01575222f9f84c244
WHIRLPOOL
9fb4d4feb3ff867866a96533231a1b8284fd5156ab142cad727d32f8f3c157e246cca59185c3bdc253b19bde2514404a7107a62443780b060f6e8f270622c990
-DIST bamtools-2.3.0.tar.gz 539446 SHA256
288046e6d5d41afdc5fce8608c5641cf2b8e670644587c1315b90bbe92f039af SHA512
432f66384cffc04ab6bc7dc66d8f7b79c1e468d0068db4cabb5cac05f9b6bef7968eff71ffb3ee51b84e23d9bb66a11ef267024138f40116c25e7f18e7210a5c
WHIRLPOOL
dd888f67c3d0b0ce2f5f2875e242e5df0d54cefd13693230b5f10eb57dd780304b601027cf65f6598a54061a7166903bf06c6c9a46939f6ce6bbb246cab89993
DIST bamtools-2.4.1.tar.gz 540482 SHA256
933a0c1a83c88c1dac8078c0c0e82f6794c75cb927265399404bc2cc2611204b SHA512
ee674014f27b2dc0aa7c0415e8654ee7c39cfdecafbd9983d970fad6ad29f070a7ff372ee05765956cf7c8f8bb3b9763b6e537e693a0d2d64680148b1a23cfee
WHIRLPOOL
6ef73f0713ebf993123eac7095061e32fe6a53db383e28a5dd8967afee92fb211ce56611de9718ce4cce84bdee14157ff968e0a6edcaead4e06b44008b78b84c
diff --git a/sci-biology/bamtools/bamtools-1.0.2-r1.ebuild
b/sci-biology/bamtools/bamtools-1.0.2-r1.ebuild
deleted file mode 100644
index dc1b60b..
--- a/sci-biology/bamtools/bamtools-1.0.2-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM
files"
-HOMEPAGE="https://github.com/pezmaster31/bamtools;
-SRC_URI="mirror://github/pezmaster31/bamtools/"${P}".tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- dev-libs/jsoncpp
- sys-libs/zlib"
-DEPEND="${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.so lib/*so*
- use static-libs && dolib.a lib/*a
- insinto /usr/include/bamtools
- doins include/api include/shared
- dodoc README
-}
diff --git a/sci-biology/bamtools/bamtools-2.3.0.ebuild
b/sci-biology/bamtools/bamtools-2.3.0.ebuild
deleted file mode 100644
index b2d7d62..
--- a/sci-biology/bamtools/bamtools-2.3.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit cmake-utils
-
-DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM
files"
-HOMEPAGE="https://github.com/pezmaster31/bamtools;
-SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz ->
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
-
-DEPEND="
- >=dev-libs/jsoncpp-0.5.0-r1
-
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/files/, sci-biology/bamtools/
commit: 72bcf8aa8b3c95da31c4ae6bf4ccec376a7ec3ea
Author: David Seifert gentoo org>
AuthorDate: Wed Dec 14 22:42:36 2016 +
Commit: David Seifert gentoo org>
CommitDate: Wed Dec 14 22:43:01 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=72bcf8aa
sci-biology/bamtools: Version bump to 2.4.1
Gentoo-bug: 550144, 596208
* Make C++ mode agnostic
* Unbundle jsoncpp and use more modern versions
Package-Manager: portage-2.3.3
sci-biology/bamtools/Manifest | 1 +
sci-biology/bamtools/bamtools-2.4.1.ebuild | 26 +++
.../files/bamtools-2.4.1-fix-build-system.patch| 209 +
.../bamtools/files/bamtools-2.4.1-fix-c++14.patch | 78
4 files changed, 314 insertions(+)
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
index 1c1972c..fa04b1b 100644
--- a/sci-biology/bamtools/Manifest
+++ b/sci-biology/bamtools/Manifest
@@ -1,2 +1,3 @@
DIST bamtools-1.0.2.tar.gz 207523 SHA256
d3ca75d2bec531f15dbc400a76afbe48d47452ce05552c88943bbce81a0862d8 SHA512
1934d40d50f3fdf2b1fcacb8b59cf954a3c791d3095649ac4f1246563e9d8d4afe385e42a2c6c383f0bb519eede401d12c71203d279b33e01575222f9f84c244
WHIRLPOOL
9fb4d4feb3ff867866a96533231a1b8284fd5156ab142cad727d32f8f3c157e246cca59185c3bdc253b19bde2514404a7107a62443780b060f6e8f270622c990
DIST bamtools-2.3.0.tar.gz 539446 SHA256
288046e6d5d41afdc5fce8608c5641cf2b8e670644587c1315b90bbe92f039af SHA512
432f66384cffc04ab6bc7dc66d8f7b79c1e468d0068db4cabb5cac05f9b6bef7968eff71ffb3ee51b84e23d9bb66a11ef267024138f40116c25e7f18e7210a5c
WHIRLPOOL
dd888f67c3d0b0ce2f5f2875e242e5df0d54cefd13693230b5f10eb57dd780304b601027cf65f6598a54061a7166903bf06c6c9a46939f6ce6bbb246cab89993
+DIST bamtools-2.4.1.tar.gz 540482 SHA256
933a0c1a83c88c1dac8078c0c0e82f6794c75cb927265399404bc2cc2611204b SHA512
ee674014f27b2dc0aa7c0415e8654ee7c39cfdecafbd9983d970fad6ad29f070a7ff372ee05765956cf7c8f8bb3b9763b6e537e693a0d2d64680148b1a23cfee
WHIRLPOOL
6ef73f0713ebf993123eac7095061e32fe6a53db383e28a5dd8967afee92fb211ce56611de9718ce4cce84bdee14157ff968e0a6edcaead4e06b44008b78b84c
diff --git a/sci-biology/bamtools/bamtools-2.4.1.ebuild
b/sci-biology/bamtools/bamtools-2.4.1.ebuild
new file mode 100644
index ..e657cc4
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-2.4.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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;
+SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz ->
${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="
+ >=dev-libs/jsoncpp-1.8.0
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.4.1-fix-build-system.patch
+ "${FILESDIR}"/${PN}-2.4.1-fix-c++14.patch
+)
diff --git a/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch
b/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch
new file mode 100644
index ..7959723
--- /dev/null
+++ b/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch
@@ -0,0 +1,209 @@
+* Unbundle jsoncpp
+* Remove forcing C++98
+* Remove forcing CMAKE_BUILD_TYPE
+* Remove -fPIC globally
+* Fix LFS macro definitions
+* Make building static library optional
+* Use GNUInstallDirs conventions
+* Install .pc file
+See also: https://bugs.gentoo.org/show_bug.cgi?id=550144
+
+Taken from https://github.com/pezmaster31/bamtools/pull/139
+
+--- a/CMakeLists.txt
b/CMakeLists.txt
+@@ -9,7 +9,14 @@
+ project( BamTools )
+
+ # Cmake requirements
+-cmake_minimum_required( VERSION 2.6.4 )
++cmake_minimum_required( VERSION 3.0 )
++
++# on macOS, MACOSX_RPATH is enabled by default on more recent versions
++# of CMake. Disable this behaviour, and let user enable it if need be.
++cmake_policy( SET CMP0042 OLD )
++
++# Adhere to GNU filesystem layout conventions
++include( GNUInstallDirs )
+
+ # Force the build directory to be different from source directory
+ macro( ENSURE_OUT_OF_SOURCE_BUILD MSG )
+@@ -34,18 +41,21 @@
+ set( BamTools_VERSION_MINOR 4 )
+ set( BamTools_VERSION_BUILD 1 )
+
+-# set our library and executable destination dirs
+-set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )
+-set( LIBRARY_OUTPUT_PATH"${CMAKE_SOURCE_DIR}/lib" )
+-
+ # define compiler flags for all code
+-set( CMAKE_BUILD_TYPE Release )
+-set( CMAKE_CXX_FLAGS_RELEASE "-std=c++98 ${CMAKE_CXX_FLAGS_RELEASE}" )
+-add_definitions( -Wall -D_FILE_OFFSET_BITS=64 )
++add_definitions( -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-D_LARGEFILE64_SOURCE )
++add_compile_options( -Wall )
+
+ # ---
+ # handle platform-/environment-specific defines
+
++# Make building the static library optional
++option( BUILD_STATIC "Build static libbamtools
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: 8deb276adb49578cf19bce5ef8fe9394aa90db6f
Author: Justin Lecher gentoo org>
AuthorDate: Sun Dec 13 09:19:12 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Sun Dec 13 09:19:12 2015 +
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 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 $i || die
done
dobin bin/bamtools
- dolib lib/*
- insinto /usr/include/bamtools/api
- doins include/api/*
- insinto /usr/include/bamtools/shared
- doins include/shared/*
+ dolib.so lib/*so*
+ use static-libs && dolib.a lib/*a
+ insinto /usr/include/bamtools
+ doins include/api include/shared
dodoc README
}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/, sci-biology/bamtools/files/
commit: 17bad73aea37d3a55e0cdff3e7e01117ea24773e
Author: Justin Lecher gentoo org>
AuthorDate: Sun Dec 13 12:25:33 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Sun Dec 13 14:05:28 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=17bad73a
sci-biology/bamtools: Add missing die and drop old patch
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher gentoo.org>
sci-biology/bamtools/bamtools-2.3.0.ebuild | 4 ++-
.../bamtools/files/bamtools-2.2.3-unbundle.patch | 32 --
2 files changed, 3 insertions(+), 33 deletions(-)
diff --git a/sci-biology/bamtools/bamtools-2.3.0.ebuild
b/sci-biology/bamtools/bamtools-2.3.0.ebuild
index 5b6468c..b2d7d62 100644
--- a/sci-biology/bamtools/bamtools-2.3.0.ebuild
+++ b/sci-biology/bamtools/bamtools-2.3.0.ebuild
@@ -25,5 +25,7 @@ PATCHES=( "${FILESDIR}"/${P}-unbundle.patch )
src_install() {
cmake-utils_src_install
- use static-libs || rm "${ED}"/usr/$(get_libdir)/*.a
+ if ! use static-libs; then
+ rm "${ED}"/usr/$(get_libdir)/*.a || die
+ fi
}
diff --git a/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch
b/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch
deleted file mode 100644
index 318396e..000
--- a/sci-biology/bamtools/files/bamtools-2.2.3-unbundle.patch
+++ /dev/null
@@ -1,32 +0,0 @@
- src/CMakeLists.txt | 1 -
- src/api/CMakeLists.txt | 4 ++--
- src/toolkit/bamtools_filter.cpp | 2 +-
- 3 files changed, 3 insertions(+), 4 deletions(-)
-
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index e359695..2bd2185 100644
a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -6,7 +6,6 @@
- # ==
-
- add_subdirectory( api )
--add_subdirectory( third_party )
- add_subdirectory( toolkit )
- add_subdirectory( utils )
-
-diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
-index 66eb35f..65f4639 100644
a/src/api/CMakeLists.txt
-+++ b/src/api/CMakeLists.txt
-@@ -54,8 +54,8 @@ target_link_libraries( BamTools ${APILibs} )
- target_link_libraries( BamTools-static ${APILibs} )
-
- # set library install destinations
--install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME
DESTINATION "bin")
--install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
-+install( TARGETS BamTools LIBRARY DESTINATION "lib${LIB_SUFFIX}" RUNTIME
DESTINATION "bin")
-+install( TARGETS BamTools-static ARCHIVE DESTINATION "lib${LIB_SUFFIX}")
-
- # export API headers
- include(../ExportHeader.cmake)
[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/
commit: 8c05129e3e2fce50f23c7c5c6015575f686f6e8f
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Sun Aug 16 11:18:23 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Sun Aug 16 11:30:22 2015 +
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}
