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commit: bb7161d41c11db40813d5ad231aeaa60b6db3b86 |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Tue Jan 22 12:17:12 2019 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Tue Jan 22 12:18:03 2019 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bb7161d4 |
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|
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sci-libs/io_lib: version bump |
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|
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Add a new version with experimental CRAM support. |
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|
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Force dependency on libdeflate although it could/should be maybe |
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protected by USE flag. However, it is recommended by upstream authors. |
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|
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https://github.com/jkbonfield/io_lib/issues/11 |
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https://github.com/jkbonfield/io_lib/issues/12 |
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https://github.com/jkbonfield/io_lib/issues/13 |
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|
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Package-Manager: Portage-2.3.56, Repoman-2.3.12 |
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Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> |
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|
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sci-libs/io_lib/io_lib-1.14.11.ebuild | 71 +++++++++++++++++++++++++++++++++++ |
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sci-libs/io_lib/io_lib-1.14.7.ebuild | 28 -------------- |
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2 files changed, 71 insertions(+), 28 deletions(-) |
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|
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diff --git a/sci-libs/io_lib/io_lib-1.14.11.ebuild b/sci-libs/io_lib/io_lib-1.14.11.ebuild |
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new file mode 100644 |
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index 000000000..73263df65 |
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--- /dev/null |
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+++ b/sci-libs/io_lib/io_lib-1.14.11.ebuild |
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@@ -0,0 +1,71 @@ |
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+# Copyright 2019 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=5 |
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+ |
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+inherit autotools-utils eutils versionator |
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+MY_PV=$(replace_all_version_separators '-') |
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+ |
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+DESCRIPTION="General purpose trace and experiment file reading/writing interface" |
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+HOMEPAGE="https://github.com/jkbonfield/io_lib |
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+ http://staden.sourceforge.net/" |
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+SRC_URI="https://github.com/jkbonfield/io_lib/archive/${PN}-${MY_PV}.tar.gz -> ${P}.tar.gz" |
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+ |
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+LICENSE="BSD" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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+IUSE="+bzip2 curl +lzma static-libs" # maybe introduce libdeflate USE flag? |
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+ |
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+S="${WORKDIR}"/"${PN}-${PN}-${MY_PV}" |
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+ |
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+# >>> Working in BUILD_DIR: "/scratch/var/tmp/portage/sci-libs/io_lib-1.14.11/work/io_lib-1.14.11_build" |
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+# /scratch/var/tmp/portage/sci-libs/io_lib-1.14.11/temp/environment: line 530: pushd: /scratch/var/tmp/portage/sci-libs/io_lib-1.14.11/work/io_lib-1.14.11_build: No such file or directory |
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+# * ERROR: sci-libs/io_lib-1.14.11::science failed (install phase): |
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+# * (no error message) |
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+# * |
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+# * Call stack: |
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+# * ebuild.sh, line 124: Called src_install |
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+# * environment, line 2506: Called autotools-utils_src_install |
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+# * environment, line 530: Called die |
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+# * The specific snippet of code: |
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+# * pushd "${BUILD_DIR}" > /dev/null || die; |
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+# |
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+BUILD_DIR="${S}" |
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+ |
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+# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. (Only |
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+# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.) |
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+#DEPEND="!sci-biology/bioperl" |
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+DEPEND=" |
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+ app-arch/libdeflate |
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+ lzma? ( app-arch/xz-utils:= app-arch/lzma ) |
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+ bzip2? ( app-arch/bzip2 ) |
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+ curl? ( net-misc/curl ) |
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+ sys-libs/zlib" |
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+RDEPEND="${DEPEND}" |
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+ |
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+src_prepare(){ |
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+ # https://github.com/jkbonfield/io_lib/issues/12 |
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+ eautoreconf |
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+ default |
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+} |
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+ |
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+src_configure(){ |
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+ # https://github.com/jkbonfield/io_lib/issues/11 |
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+ # https://github.com/jkbonfield/io_lib/issues/13 |
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+ local myconf=() |
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+ ! use static-libs && myconf+=( "--enable-static=no" ) |
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+ econf ${myconf[@]} $(use_with libdeflate) |
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+} |
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+ |
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+src_compile(){ |
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+ # BUG: "have to" provide my own src_compile() because ${P}_build dir is missing now |
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+ # alternatively BUILD_DIR="${S}" would probably help here too |
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+ emake |
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+} |
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+ |
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+src_install() { |
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+ # cd "${S}" || die # this does not help to get around the ${P}_build missing |
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+ # what helped was to set BUILD_DIR="${S}" above |
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+ autotools-utils_src_install |
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+ dodoc docs/{Hash_File_Format,ZTR_format} |
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+} |
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|
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diff --git a/sci-libs/io_lib/io_lib-1.14.7.ebuild b/sci-libs/io_lib/io_lib-1.14.7.ebuild |
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deleted file mode 100644 |
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index d76cffe92..000000000 |
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--- a/sci-libs/io_lib/io_lib-1.14.7.ebuild |
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+++ /dev/null |
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@@ -1,28 +0,0 @@ |
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-# Copyright 1999-2016 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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- |
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-EAPI=5 |
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- |
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-inherit autotools-utils |
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- |
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-DESCRIPTION="General purpose trace and experiment file reading/writing interface" |
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-HOMEPAGE="http://staden.sourceforge.net/" |
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-SRC_URI="mirror://sourceforge/staden/${P}.tar.gz" |
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- |
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-LICENSE="BSD" |
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-SLOT="0" |
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-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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-IUSE="static-libs" |
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- |
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-# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. (Only |
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-# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.) |
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-#DEPEND="!sci-biology/bioperl" |
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-DEPEND=" |
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- net-misc/curl |
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- sys-libs/zlib" |
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-RDEPEND="${DEPEND}" |
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- |
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-src_install() { |
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- autotools-utils_src_install |
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- dodoc docs/{Hash_File_Format,ZTR_format} |
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-} |