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