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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-26 23:13:52 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-26 23:13:52 +0100 |
| commit | db6617fcd21401115d88ef59b233ae5430650d18 (patch) | |
| tree | 6c70134e0d8731cad2ec9fb5ea629606f6ea1998 /sci-biology | |
| parent | sci-biology/flexbar: remove spaces (diff) | |
| download | sci-db6617fcd21401115d88ef59b233ae5430650d18.tar.gz sci-db6617fcd21401115d88ef59b233ae5430650d18.tar.bz2 sci-db6617fcd21401115d88ef59b233ae5430650d18.zip | |
sci-biology/gbench and sci-biology/ncbi-tools++: do not download ncbi-vdb
Do not download sources from github during configure phase. This disables
the feature completely. Somehow it does not find vdb binaries provided
by our sci-biology/ncbi-tools++ package?
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/gbench/gbench-2.10.7.ebuild | 20 | ||||
| -rw-r--r-- | sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 5 |
2 files changed, 22 insertions, 3 deletions
diff --git a/sci-biology/gbench/gbench-2.10.7.ebuild b/sci-biology/gbench/gbench-2.10.7.ebuild index 4c57d1656..48e7f9d68 100644 --- a/sci-biology/gbench/gbench-2.10.7.ebuild +++ b/sci-biology/gbench/gbench-2.10.7.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -34,6 +34,7 @@ RDEPEND="${PYTHON_DEPS} media-libs/freetype media-libs/giflib media-libs/tiff:0= + || ( sci-biology/ncbi-tools++ sci-biology/sra_sdk ) gnutls? ( net-libs/gnutls ) hdf5? ( sci-libs/hdf5 ) sys-fs/fuse @@ -70,6 +71,19 @@ src_configure(){ # configure: error: --datadir=/usr/share: unknown option; use --help to show usage # configure: error: --sysconfdir=/etc: unknown option; use --help to show usage # configure: error: --localstatedir=/var/lib: unknown option; use --help to show usage - ./configure --prefix="${DESTDIR}"/"${EPREFIX}/usr" --libdir="${EPREFIX}/usr/$(get_libdir)" CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" || die + ./configure --prefix="${DESTDIR}"/"${EPREFIX}/usr" --libdir="${EPREFIX}/usr/$(get_libdir)" \ + --without-downloaded-vdb \ + CC="$(tc-getCC)" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" || die } + +# Doh, it runs git during configure phase if it could not find NCBI SRA VDB +# by executing ./scripts/common/add_vdb.sh which points to https://github.com/ncbi/ncbi-vdb +# But, we already have sci-biology/sra_sdk which blocks sci-biology/ncbi-tools++ +# as some file overlap. Seems ncbi-vdb is yet another smaller subset of either +# of the two? +# +# Same come checking out ncbi-vdb should be in ncbi-tools++-18.0.0 . +# +# That behavior is entirely optional; you can suppress it by +# configuring the Toolkit --without-downloaded-vdb, --with-vdb=PATH (e.g., +# --with-vdb=/usr), or --without-vdb altogether. diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 179baeaea..5c91c1b0c 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -220,6 +220,11 @@ src_configure() { --without-sybase --with-autodep # --with-3psw=std:netopt favor standard (system) builds of the above pkgs + # preventing executing git to checkout during configure phase ncbi-vdb sources + # resulting in 'checking for ncbi-vdb... no' and + # '^PACKAGES:' + # '^ disabled: ... VDB' + --without-downloaded-vdb $(use_with debug) $(use_with debug max-debug) $(use_with debug symbols) |