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commit: 22fd8327e252d7cf356f2337cafed02bef31a42d |
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Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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AuthorDate: Tue Jan 29 21:23:35 2013 +0000 |
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Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
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CommitDate: Tue Jan 29 21:23:35 2013 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=22fd8327 |
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|
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my version |
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|
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Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
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|
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--- |
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.../ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 345 ++++++++++++++++++++ |
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1 files changed, 345 insertions(+), 0 deletions(-) |
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|
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diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild |
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new file mode 100644 |
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index 0000000..9806b41 |
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--- /dev/null |
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+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild |
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@@ -0,0 +1,345 @@ |
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+# Copyright 1999-2012 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-0.2010.06.15-r1.ebuild,v 1.3 2012/11/05 11:22:49 jlec Exp $ |
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+ |
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+EAPI=5 |
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+ |
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+inherit eutils flag-o-matic multilib toolchain-funcs |
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+ |
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+MY_TAG="Jun_15_2010" |
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+MY_Y="${MY_TAG/*_/}" |
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+MY_PV="9_0_0" |
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+MY_P="ncbi_cxx--${MY_PV}" |
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+#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz |
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+ |
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+ |
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+DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" |
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+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit" |
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+SRC_URI=" |
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+ ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz" |
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+# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" |
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+ |
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+LICENSE="public-domain" |
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+SLOT="0" |
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+IUSE=" |
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+ debug static-libs static threads pch |
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+ test wxwidgets odbc |
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+ berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif |
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+ glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python |
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+ sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X" |
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+#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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+KEYWORDS="" |
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+ |
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+# sys-libs/db should be compiled with USE=cxx |
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+DEPEND=" |
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+ berkdb? ( sys-libs/db:4.3[cxx] ) |
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+ ftds? ( dev-db/freetds ) |
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+ boost? ( dev-libs/boost ) |
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+ curl? ( net-misc/curl ) |
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+ sqlite? ( dev-db/sqlite ) |
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+ sqlite3? ( dev-db/sqlite:3 ) |
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+ mysql? ( virtual/mysql ) |
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+ gnutls? ( net-libs/gnutls ) |
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+ ssl? ( dev-libs/openssl ) |
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+ fltk? ( x11-libs/fltk ) |
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+ opengl? ( virtual/opengl ) |
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+ mesa? ( media-libs/mesa ) |
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+ glut? ( media-libs/freeglut ) |
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+ freetype? ( media-libs/freetype ) |
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+ fastcgi? ( www-apache/mod_fastcgi ) |
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+ python? ( dev-lang/python ) |
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+ cppunit? ( dev-util/cppunit ) |
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+ icu? ( dev-libs/icu ) |
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+ expat? ( dev-libs/expat ) |
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+ sablotron? ( app-text/sablotron ) |
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+ xml? ( dev-libs/libxml2 ) |
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+ xslt? ( dev-libs/libxslt ) |
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+ xerces? ( dev-libs/xerces-c ) |
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+ xalan? ( dev-libs/xalan-c ) |
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+ muparser? ( dev-cpp/muParser ) |
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+ hdf5? ( sci-libs/hdf5 ) |
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+ gif? ( media-libs/giflib ) |
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+ jpeg? ( virtual/jpeg ) |
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+ png? ( media-libs/libpng ) |
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+ tiff? ( media-libs/tiff ) |
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+ xpm? ( x11-libs/libXpm ) |
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+ dev-libs/lzo |
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+ app-arch/bzip2 |
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+ dev-libs/libpcre" |
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+# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge |
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+ |
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+# configure options, may want to expose some |
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+# --without-debug build non-debug versions of libs and apps |
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+# --without-optimization turn off optimization flags in non-debug mode |
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+# --with-profiling build profiled versions of libs and apps |
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+# --with-tcheck(=DIR) build for Intel Thread Checker (in DIR) |
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+# --with-dll build all libraries as DLLs |
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+# --with-static build all libraries statically even if --with-dll |
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+# --with-static-exe build all executables as statically as possible |
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+# --with-plugin-auto-load always enable the plugin manager by default |
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+# --with-bin-release build executables suitable for public release |
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+# --with-mt compile in a MultiThread-safe manner |
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+# --with-64 compile to 64-bit code |
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+# --with-universal build universal binaries on Mac OS X |
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+# --with-universal=CPUs build universal binaries targeting the given CPUs |
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+# --without-exe do not build executables |
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+# --with-runpath= hard-code the runtime path to DLLs |
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+# --with-lfs enable large file support to the extent possible |
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+# --with-extra-action= script to call after the configuration is complete |
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+# --with-autodep automatic generation of dependencies (GNU make) |
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+# --with-build-root=DIR specify a non-default build directory name |
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+# --with-fake-root=DIR appear to have been built under DIR |
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+# --without-suffix no Release/Debug, MT or DLL sfx in the build dir name |
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+# --with-hostspec add full host specs to the build dir name |
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+# --without-version don't always include the cplr ver in the bd name |
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+# --with-build-root-sfx=X add a user-specified suffix to the build dir name |
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+# --without-execopy do not copy built executables to the BIN area |
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+# --with-bincopy populate lib and bin with copies, not hard links |
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+# --with-lib-rebuilds ensure that apps use up-to-date libraries |
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+# --with-lib-rebuilds=ask ask whether to update each app's libraries |
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+# --without-deactivation keep old copies of libraries that no longer build |
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+# --without-makefile-auto-update do not auto-update generated makefiles |
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+# --with-projects=FILE build projects listed in FILE by default |
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+# --without-flat-makefile do not generate an all-encompassing flat makefile |
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+# --with-configure-dialog allow interactive flat makefile project selection |
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+# --with-saved-settings=F load configuration settings from the file F |
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+# --with-check run test suite after the build |
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+# --with-check-tools=... use the specified tools for testing |
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+# --with-ncbi-public ensure compatibility for all in-house platforms |
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+# --with-strip strip binaries at build time |
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+# --with-pch use precompiled headers if possible |
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+# --with-caution cancel configuration unconditionally when in doubt |
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+# --without-caution proceed without asking when in doubt |
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+# --without-ccache do not automatically use ccache if available |
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+# --without-distcc do not automatically use distcc if available |
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+# --without-ncbi-c do not use NCBI C Toolkit |
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+# --without-sss do not use NCBI SSS libraries |
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+# --without-utils do not use NCBI SSS UTIL library |
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+# --without-sssdb do not use NCBI SSS DB library |
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+# --with-included-sss use the in-tree copy of SSS |
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+ |
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+# --without-local-lbsm turn off support for IPC with locally running LBSMD |
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+# --without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt |
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+# --without-connext do not build non-public CONNECT library extensions |
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+# --without-serial do not build the serialization library and tools |
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+# --without-objects do not generate/build serializeable objects from ASNs |
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+# --without-dbapi do not build database connectivity libraries |
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+# --without-app do not build standalone applications like ID1_FETCH |
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+# --without-ctools do not build NCBI C Toolkit based projects |
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+# --without-gui do not build most graphical projects |
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+# --without-algo do not build CPU-intensive algorithms |
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+# --without-internal do not build internal projects |
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+# --with-gbench ensure that Genome Workbench can be built |
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+# --without-gbench do not build Genome Workbench |
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+ |
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+RDEPEND="${DEPEND}" |
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+ |
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+S="${WORKDIR}/${MY_P}" |
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+ |
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+src_prepare() { |
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+# filter-ldflags -Wl,--as-needed |
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+# append-ldflags -Wl,--no-undefined |
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+# sed -i -e 's/-print-file-name=libstdc++.a//' \ |
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+# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ |
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+# src/build-system/configure || die |
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+# epatch \ |
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+# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ |
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+# "${FILESDIR}"/curl-types.patch \ |
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+# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ |
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+# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ |
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+# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ |
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+# "${FILESDIR}"/report_project_settings_configure.ac.patch \ |
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+# "${FILESDIR}"/report_project_settings_configure.patch \ |
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+# "${FILESDIR}"/make_install.patch |
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+ |
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+# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch |
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+ |
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+ |
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+# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ |
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+# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ |
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+# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ |
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+# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ |
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+# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch |
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+ |
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+# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" |
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+ tc-export CXX CC |
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+} |
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+ |
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+src_configure() { |
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+ local myconf=() |
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+ #--without-optimization turn off optimization flags in non-debug mode |
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+ #--with-profiling build profiled versions of libs and apps |
193 |
+ #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) |
194 |
+ #--with-plugin-auto-load always enable the plugin manager by default |
195 |
+ #--with-bundles build bundles in addition to dylibs on Mac OS X |
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+ #--with-bin-release build executables suitable for public release |
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+ # no dll and such |
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+ #--with-64 compile to 64-bit code |
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+ # --with-universal build universal binaries on Mac OS X |
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+ # --with-universal=CPUs build universal binaries targeting the given CPUs |
201 |
+ # --without-exe do not build executables |
202 |
+ #--with-relative-runpath=P specify an executable-relative DLL search path |
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+ # --with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH |
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+ # --with-limited-linker don't attempt to build especially large projects |
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+ #--with-extra-action= script to call after the configuration is complete |
206 |
+ #--with-autodep automatic generation of dependencies (GNU make) |
207 |
+ # --with-fake-root=DIR appear to have been built under DIR |
208 |
+ #--with-build-root-sfx=X add a user-specified suffix to the build dir name |
209 |
+ # --without-execopy do not copy built executables to the BIN area |
210 |
+ #--with-lib-rebuilds ensure that apps use up-to-date libraries |
211 |
+ # --with-lib-rebuilds=ask ask whether to update each app's libraries |
212 |
+ # --without-deactivation keep old copies of libraries that no longer build |
213 |
+ # --without-makefile-auto-update do not auto-update generated makefiles |
214 |
+ # --with-projects=FILE build projects listed in FILE by default |
215 |
+ # --without-flat-makefile do not generate an all-encompassing flat makefile |
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+ # --with-configure-dialog allow interactive flat makefile project selection |
217 |
+ # --with-saved-settings=F load configuration settings from the file F |
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+ #-with-check-tools=... use the specified tools for testing |
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+ # --with-ncbi-public ensure compatibility for all in-house platforms |
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+ #--with-sybase-local=DIR use local SYBASE install (DIR is optional) |
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+ # --with-sybase-new use newer SYBASE install (12.5 rather than 12.0) |
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+ #--without-ftds-renamed do not rename Sybase DBLIB symbols in built-in FTDS |
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+ #--without-sp do not use SP libraries |
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+ #--without-orbacus do not use ORBacus CORBA libraries |
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+ # --with-orbacus=DIR use ORBacus installation in DIR |
226 |
+ #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) |
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+ #--with-sablot=DIR use Sablotron installation in DIR |
228 |
+ # --without-sablot, do not use Sablotron |
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+ #--with-oechem=DIR use OpenEye OEChem installation in DIR |
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+ # --without-oechem do not use OEChem |
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+ # --with-sge=DIR use Sun Grid Engine installation in DIR |
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+ # --without-sge do not use Sun Grid Engine |
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+ #--with-magic=DIR use libmagic installation in DIR |
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+ # --without-magic do not use libmagic |
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+ #--without-local-lbsm turn off support for IPC with locally running LBSMD |
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+ # --without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt |
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+ # --without-connext do not build non-public CONNECT library extensions |
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+ # --without-serial do not build the serialization library and tools |
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+ # --without-objects do not generate/build serializeable objects from ASNs |
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+ # --without-dbapi do not build database connectivity libraries |
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+ # --without-app do not build standalone applications like ID1_FETCH |
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+ # --without-gui do not build most graphical projects |
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+ # --without-algo do not build CPU-intensive algorithms |
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+ #--without-internal do not build internal projects |
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+ # --with-gbench ensure that Genome Workbench can be built |
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+ # --without-gbench do not build Genome Workbench |
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+ myconf+=( |
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+ --with-dll |
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+ --with-lfs |
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+ --with-build-root="${S}"_build |
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+ --without-suffix |
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+ --without-hostspec |
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+ --without-version |
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+ --with-bincopy |
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+ --without-strip |
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+ --without-ccache |
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+ --without-distcc |
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+ --with-ncbi-c |
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+ --without-ctools |
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+ --with-sss |
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+ --with-utils |
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+ --with-sssdb |
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+ --with-included-sss |
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+ --with-z="${EPREFIX}"/usr |
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+ --with-bz2="${EPREFIX}"/usr |
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+ --with-muparser="${EPREFIX}"/usr |
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+ --without-sybase |
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+# --with-3psw=std:netopt |
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+ $(use_with debug) |
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+ $(use_with debug max-debug) |
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+ $(use_with debug symbols) |
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+ $(use_with static-libs static) |
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+ $(use_with static static-exe) |
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+ $(use_with threads mt) |
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+ $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx") |
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+ $(use_with test check) |
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+ $(use_with pch) |
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+ $(use_with lzo lzo "${EPREFIX}"/usr) |
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+ $(use_with pcre pcre "${EPREFIX}"/usr) |
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+ $(use_with gnutls gnutls "${EPREFIX}"/usr) |
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+ $(use_with ssl openssl "${EPREFIX}"/usr) |
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+ $(use_with ftds ftds "${EPREFIX}"/usr) |
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+ $(use_with mysql mysql "${EPREFIX}"/usr) |
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+ $(use_with fltk fltk "${EPREFIX}"/usr) |
285 |
+ $(use_with opengl opengl "${EPREFIX}"/usr) |
286 |
+ $(use_with mesa mesa "${EPREFIX}"/usr) |
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+ $(use_with opengl glut "${EPREFIX}"/usr) |
288 |
+ $(use_with opengl glew "${EPREFIX}"/usr) |
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+ $(use_with opengl glew-m) |
290 |
+ $(use_with wxwidgets wxwidgets "${EPREFIX}"/usr) |
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+ $(use_with wxwidgets wxwidgets-ucs) |
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+ $(use_with freetype freetype "${EPREFIX}"/usr) |
293 |
+ $(use_with fastcgi fastcgi "${EPREFIX}"/usr) |
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+ $(use_with berkdb bdb "${EPREFIX}"/usr) |
295 |
+ $(use_with odbc odbc "${EPREFIX}"/usr) |
296 |
+ $(use_with python python "${EPREFIX}"/usr) |
297 |
+ $(use_with boost boost "${EPREFIX}"/usr) |
298 |
+ $(use_with sqlite sqlite3 "${EPREFIX}"/usr) |
299 |
+ $(use_with icu icu "${EPREFIX}"/usr) |
300 |
+ $(use_with expat expat "${EPREFIX}"/usr) |
301 |
+ $(use_with xml libxml2 "${EPREFIX}"/usr) |
302 |
+ $(use_with xml libxslt "${EPREFIX}"/usr) |
303 |
+ $(use_with xerces xerces "${EPREFIX}"/usr) |
304 |
+ $(use_with hdf5 hdf5 "${EPREFIX}"/usr) |
305 |
+ $(use_with xalan xalan "${EPREFIX}"/usr) |
306 |
+ $(use_with gif gif "${EPREFIX}"/usr) |
307 |
+ $(use_with jpeg jpeg "${EPREFIX}"/usr) |
308 |
+ $(use_with tiff tiff "${EPREFIX}"/usr) |
309 |
+ $(use_with png png "${EPREFIX}"/usr) |
310 |
+ $(use_with xpm xpm "${EPREFIX}"/usr) |
311 |
+ $(use_with curl curl "${EPREFIX}"/usr) |
312 |
+ $(use_with X x "${EPREFIX}"/usr) |
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+ ) |
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+ |
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+ # http://www.ncbi.nlm.nih.gov/books/NBK7167/ |
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+ use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) |
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+ |
318 |
+ # TODO |
319 |
+ # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure |
320 |
+ # otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9 |
321 |
+ |
322 |
+ "${S}"/configure \ |
323 |
+ --prefix="${EPREFIX}"/usr \ |
324 |
+ --build=x86_64-pc-linux-gnu \ |
325 |
+ --host=x86_64-pc-linux-gnu \ |
326 |
+ --infodir=/usr/share/info \ |
327 |
+ --datadir=/usr/share \ |
328 |
+ --sysconfdir=/etc \ |
329 |
+ --localstatedir=/var/lib \ |
330 |
+ --libdir=/usr/lib64 \ |
331 |
+ ${myconf[@]} || die |
332 |
+#--without-debug \ |
333 |
+# --with-bin-release \ |
334 |
+# --with-bincopy \ |
335 |
+# --without-static \ |
336 |
+# --with-dll \ |
337 |
+# --with-mt \ |
338 |
+# --with-lfs \ |
339 |
+# --prefix="${ED}"/usr \ |
340 |
+# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ |
341 |
+# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ |
342 |
+# || die |
343 |
+# econf ${myconf[@]} |
344 |
+} |
345 |
+ |
346 |
+src_compile() { |
347 |
+ # all_r would ignore the --with-projects contents and build more |
348 |
+ # emake all_r -C GCC*-Release*/build || die |
349 |
+ # all_p with compile only selected/required components |
350 |
+ emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" |
351 |
+} |
352 |
+ |
353 |
+src_install() { |
354 |
+ emake install || die |
355 |
+ # File collisions with sci-biology/ncbi-tools |
356 |
+ rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp} |
357 |
+ mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2 |
358 |
+ |
359 |
+ echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} |
360 |
+ doenvd "${S}/99${PN}" |
361 |
+} |
362 |
+ |
363 |
+pkg_postinst() { |
364 |
+ einfo 'Please run "source /etc/profile" before using this package in the current shell.' |
365 |
+ einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' |
366 |
+} |