commit: d02fe7fbe1b779c21cf1fed579d8fc4494f967d5 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Mon Jan 18 15:32:24 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Mon Jan 18 15:32:24 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d02fe7fb
sci-biology/staden: EAPI bump Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/staden/staden-2.0.0_beta10.ebuild | 84 --------------------------- sci-biology/staden/staden-2.0.0_beta11.ebuild | 30 ++++------ sci-biology/staden/staden-9999.ebuild | 45 +++++--------- 3 files changed, 26 insertions(+), 133 deletions(-) diff --git a/sci-biology/staden/staden-2.0.0_beta10.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild deleted file mode 100644 index 53c4d2212..000000000 --- a/sci-biology/staden/staden-2.0.0_beta10.ebuild +++ /dev/null @@ -1,84 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -AUTOTOOLS_AUTORECONF=yes - -inherit autotools-utils eutils flag-o-matic fortran-2 multilib - -DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" -HOMEPAGE="https://sourceforge.net/projects/staden"; -SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz"; - -LICENSE="staden" -SLOT="0" -KEYWORDS="" -IUSE="debug doc fortran png tcl tk X zlib" - -# either g77 or gfortran must be available -# edit src/mk/linux.mk accordingly -# -# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 -# -# -# - -DEPEND=" - app-arch/xz-utils - dev-lang/tk:0= - dev-tcltk/tklib - media-libs/libpng:0 - sci-biology/samtools:0 - >=sci-libs/io_lib-1.13.8 - sys-libs/zlib" -RDEPEND="${DEPEND} - >=dev-tcltk/iwidgets-4.0 - tcl? ( >=dev-tcltk/itcl-3.2 ) - tk? ( >=dev-tcltk/itk-3.2 ) - net-misc/curl - doc? ( sci-biology/staden_doc )" - -S="${WORKDIR}"/staden-${PV/_beta/b}-src - -AUTOTOOLS_IN_SOURCE_BUILD=1 - -PATCHES=( - "${FILESDIR}"/${P}-ldflags.patch - "${FILESDIR}"/${P}-zlib.patch ) - -src_prepare() { - sed \ - -e 's:svnversion:false:' \ - -i configure.in || die - - AT_M4DIR=ac_stubs autotools-utils_src_prepare -} - -src_configure(){ - local myeconfargs=() - use X && myeconfargs+=( --with-x ) - myeconfargs+=( - --with-tklib=/usr/$(get_libdir)/tklib - ) - use amd64 && myeconfargs+=( --enable-64bit ) - use debug && append-cflags "-DCACHE_REF_DEBUG" - autotools-utils_src_configure -} - -src_install() { - autotools-utils_src_install - # install the LDPATH so that it appears in /etc/ld.so.conf after env-update - # subsequently, apps linked against /usr/lib/staden can be run because - # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' - # somehow for gap2caf, for example - cat >> "${T}"/99staden <<- EOF - STADENROOT="${EPREFIX}"/usr/share/staden - LDPATH="${EPREFIX}/usr/$(get_libdir)/staden" - EOF - doenvd "${T}"/99staden -} - -pkg_postinst(){ - einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"; -} diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild index b8e5425c7..523f8bf05 100644 --- a/sci-biology/staden/staden-2.0.0_beta11.ebuild +++ b/sci-biology/staden/staden-2.0.0_beta11.ebuild @@ -1,11 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -AUTOTOOLS_AUTORECONF=yes - -inherit autotools-utils eutils flag-o-matic fortran-2 multilib +inherit flag-o-matic fortran-2 multilib DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" HOMEPAGE="https://sourceforge.net/projects/staden"; @@ -41,31 +39,27 @@ RDEPEND="${DEPEND} S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src -AUTOTOOLS_IN_SOURCE_BUILD=1 - -PATCHES=("${FILESDIR}"/${P}-ldflags.patch) +PATCHES=( + "${FILESDIR}"/${P}-ldflags.patch +) src_prepare() { + default sed \ -e 's:svnversion:false:' \ -i configure.in || die - - AT_M4DIR=ac_stubs autotools-utils_src_prepare } src_configure(){ - local myeconfargs=() - use X && myeconfargs+=( --with-x ) - myeconfargs+=( - --with-tklib=/usr/$(get_libdir)/tklib - ) - use amd64 && myeconfargs+=( --enable-64bit ) use debug && append-cflags "-DCACHE_REF_DEBUG" - autotools-utils_src_configure + econf \ + $(use_enable X x) + $(use_enable amd64 64bit) + --with-tklib=/usr/$(get_libdir)/tklib } src_install() { - autotools-utils_src_install + default # install the LDPATH so that it appears in /etc/ld.so.conf after env-update # subsequently, apps linked against /usr/lib/staden can be run because # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild index 961155bf6..c18aea8cc 100644 --- a/sci-biology/staden/staden-9999.ebuild +++ b/sci-biology/staden/staden-9999.ebuild @@ -1,11 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -AUTOTOOLS_AUTORECONF=yes - -inherit autotools-utils flag-o-matic fortran-2 multilib subversion +inherit flag-o-matic fortran-2 multilib subversion DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" HOMEPAGE="https://sourceforge.net/projects/staden/"; @@ -38,42 +36,27 @@ RDEPEND="${DEPEND} net-misc/curl doc? ( sci-biology/staden_doc )" -AUTOTOOLS_IN_SOURCE_BUILD=1 - src_prepare() { - cd "${WORKDIR}"/"${P}"/src || die + default sed \ -e 's:svnversion:false:' \ -i configure.in || die - - AT_M4DIR=ac_stubs autotools-utils_src_prepare } -src_configure() { - cd "${WORKDIR}"/"${P}"/src || die - S="${WORKDIR}"/"${P}"/src - local myeconfargs=() - use X && myeconfargs+=( --with-x ) - myeconfargs+=( - --with-tklib=/usr/$(get_libdir)/tklib - ) - use amd64 && myeconfargs+=( --enable-64bit ) +src_configure(){ use debug && append-cflags "-DCACHE_REF_DEBUG" - autotools-utils_src_configure - # edit system.mk to place there proper version number of the svn-controlled checkout - sed -e "s/^SVNVERS.*/SVNVERS = "${ESVN_REVISION}"/" -i system.mk || die -} - -src_compile(){ - cd "${WORKDIR}"/"${P}"/src || die - S="${WORKDIR}"/"${P}"/src - default + econf \ + $(use_enable X x) + $(use_enable amd64 64bit) + --with-tklib=/usr/$(get_libdir)/tklib } src_install() { - cd "${WORKDIR}"/"${P}"/src || die - S="${WORKDIR}"/"${P}"/src - autotools-utils_src_install SVN_VERSION="${ESVN_REVISION}" + default + # install the LDPATH so that it appears in /etc/ld.so.conf after env-update + # subsequently, apps linked against /usr/lib/staden can be run because + # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' + # somehow for gap2caf, for example cat >> "${T}"/99staden <<- EOF STADENROOT="${EPREFIX}"/usr/share/staden LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
