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commit: 220946d413cfcfa399e3609f2b215eabdc8df3a8 |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Sat Mar 30 00:13:51 2019 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Sat Mar 30 00:13:51 2019 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=220946d4 |
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|
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sci-biology/ncbi-tools++: version bump |
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|
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It does not link if older version is installed because linker |
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picks up older version of libraries and obviously does not find |
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newly added functions. |
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|
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Upstream says: |
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Please try either supplying an LD_RUN_PATH environment setting |
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or a -Wl,-rpath-link,... flag pointing at your build tree's lib |
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directory. Also, please bear in mind that adding the old |
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installation's library directory to the central search path largely |
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defeats the purpose of making it a separate directory. |
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|
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Package-Manager: Portage-2.3.62, 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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.../ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 380 +++++++++++++++++++++ |
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1 file changed, 380 insertions(+) |
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|
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diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild |
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new file mode 100644 |
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index 000000000..585042f9f |
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--- /dev/null |
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+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild |
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@@ -0,0 +1,380 @@ |
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+# Copyright 1999-2019 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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+PYTHON_COMPAT=( python2_7 ) |
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+ |
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+inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs |
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+ |
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+MY_TAG="Mar_28_2019" |
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+MY_Y="${MY_TAG/*_/}" |
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+MY_PV="22_0_0" |
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+MY_P="ncbi_cxx--${MY_PV}" |
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+ |
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+# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ |
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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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+# https://ncbi.github.io/cxx-toolkit/pages/release_notes |
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+SRC_URI=" |
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+ ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/${MY_TAG}/ncbi_cxx--${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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+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz |
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+# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html |
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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 gif |
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+ glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python |
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+ sablotron sqlite tiff xerces xalan xml xpm xslt X" |
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+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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+ |
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+REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
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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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+ !sci-biology/sra_sdk |
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+ app-arch/cpio |
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+ berkdb? ( sys-libs/db:4.3[cxx] ) |
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+ boost? ( dev-libs/boost ) |
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+ curl? ( net-misc/curl ) |
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+ sqlite? ( >=dev-db/sqlite-3.6.6:3 ) |
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+ mysql? ( virtual/mysql ) |
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+ fltk? ( x11-libs/fltk ) |
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+ opengl? ( virtual/opengl media-libs/glew:0= ) |
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+ mesa? ( media-libs/mesa[osmesa] ) |
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+ glut? ( media-libs/freeglut ) |
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+ freetype? ( media-libs/freetype ) |
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+ gnutls? ( net-libs/gnutls ) |
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+ python? ( ${PYTHON_DEPS} ) |
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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-1.1.14 ) |
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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[cxx] ) |
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+ gif? ( media-libs/giflib ) |
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+ jpeg? ( virtual/jpeg:0= ) |
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+ png? ( media-libs/libpng:0= ) |
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+ tiff? ( media-libs/tiff:0= ) |
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+ xpm? ( x11-libs/libXpm ) |
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+ >=dev-libs/lzo-2.0 |
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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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+# Intentionally omitted USE flags: |
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+# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. |
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+# The default (heavily patched) embedded copy should work, or you can |
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+# leave it off altogether -- the only public apps that make use of it are |
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+# samples and tests, since NCBI's database servers are of course firewalled. |
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+ |
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+# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) |
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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}-${PV#0.}-disable_test_compress.patch |
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+ |
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+# "${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)/${PN}" |
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+ |
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+# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers |
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+# local PATCHES=( |
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+# "${FILESDIR}"/${P}-configure.patch |
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+# "${FILESDIR}"/${P}-fix-install.patch |
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+# "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 |
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+# "${FILESDIR}"/${P}-fix-annotwriter-linking.patch |
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+# "${FILESDIR}"/${P}-fix-undefined-xobjread.patch |
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+# "${FILESDIR}"/${P}-fix-apps-blast-linking.patch |
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+# "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch |
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+# "${FILESDIR}"/${P}-fix-app-compartp-linking.patch |
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+# "${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch |
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+# "${FILESDIR}"/${P}-fix-app-hfilter-linking.patch |
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+# "${FILESDIR}"/${P}-fix-app-igblast-linking.patch |
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+# "${FILESDIR}"/${P}-fix-ncfetch-linking.patch |
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+# "${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch |
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+# "${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch |
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+# "${FILESDIR}"/${P}-fix-speedtest-linking.patch |
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+# "${FILESDIR}"/${P}-fix-splign-linking.patch |
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+# "${FILESDIR}"/${P}-fix-srcchk-linking.patch |
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+# "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch |
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+# "${FILESDIR}"/${P}-remove-old-symlinks.patch |
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+# "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch |
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+# "${FILESDIR}"/${P}-fix-app-tls-linking.patch |
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+# "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch |
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+# "${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch |
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+# ) |
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+ #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch |
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+# epatch ${PATCHES[@]} |
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+ # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 |
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+ # https://bugs.gentoo.org/show_bug.cgi?id=514706 |
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+ |
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+ tc-export CXX CC |
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+ |
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+ cd src/build-system || die |
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+# eautoreconf |
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+ |
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+ # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch |
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+ # eautoconf # keep it disabled until we can ensure 2.59 is installed |
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+ # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support |
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+} |
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+ |
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+# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site |
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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 |
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+ #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) |
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+ #--with-plugin-auto-load always enable the plugin manager by default |
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+ #--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 |
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+ #--without-exe do not build executables |
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+ #--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 |
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+ #--with-autodep automatic generation of dependencies (GNU make) |
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+ #--with-fake-root=DIR appear to have been built under DIR |
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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-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-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-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 |
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+ #--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 |
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+ #--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-sssutils |
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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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+ --without-sybase |
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+ --with-autodep |
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+# --with-3psw=std:netopt favor standard (system) builds of the above pkgs |
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+ # --without-downloaded-vdb is not available in 12.0.0 release yet |
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+ # preventing executing git to checkout during configure phase ncbi-vdb sources |
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+ # resulting in 'checking for ncbi-vdb... no' and |
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+ # '^PACKAGES:' |
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+ # '^ disabled: ... VDB' |
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+ --without-downloaded-vdb |
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+ $(use_with debug) |
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+# $(use_with debug max-debug) # broken in 22.0.0 as it triggers need for https://github.com/google/sanitizers/wiki/AddressSanitizer |
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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/$(get_libdir)/${PN}") |
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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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+ $(use_with mysql mysql "${EPREFIX}/usr") |
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+ $(use_with muparser muparser "${EPREFIX}/usr") |
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+ $(usex fltk --with-fltk="${EPREFIX}/usr" "") |
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+ $(use_with opengl opengl "${EPREFIX}/usr") |
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+ $(use_with mesa mesa "${EPREFIX}/usr") |
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+ $(use_with opengl glut "${EPREFIX}/usr") |
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+ $(use_with opengl glew "${EPREFIX}/usr") |
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+ $(use_with opengl glew-mx) |
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+ $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") |
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+ $(use_with wxwidgets wxwidgets-ucs) |
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+ $(use_with freetype freetype "${EPREFIX}/usr") |
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+ $(use_with fastcgi fastcgi "${EPREFIX}/usr") |
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+ $(use_with berkdb bdb "${EPREFIX}/usr") |
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+ $(usex odbc --with-odbc="${EPREFIX}/usr" "") |
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+ $(use_with python python "${EPREFIX}/usr") |
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+ $(use_with boost boost "${EPREFIX}/usr") |
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+ $(use_with sqlite sqlite3 "${EPREFIX}/usr") |
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+ $(use_with icu icu "${EPREFIX}/usr") |
299 |
+ $(use_with expat expat "${EPREFIX}/usr") |
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+ $(use_with xml libxml "${EPREFIX}/usr") |
301 |
+ $(use_with xml libxslt "${EPREFIX}/usr") |
302 |
+ $(use_with xerces xerces "${EPREFIX}/usr") |
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+ $(use_with hdf5 hdf5 "${EPREFIX}/usr") |
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+ $(use_with xalan xalan "${EPREFIX}/usr") |
305 |
+# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" |
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+ --without-gif |
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+ $(use_with jpeg jpeg "${EPREFIX}/usr") |
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+ $(use_with tiff tiff "${EPREFIX}/usr") |
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+ $(use_with png png "${EPREFIX}/usr") |
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+ $(use_with xpm xpm "${EPREFIX}/usr") |
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+ $(use_with curl curl "${EPREFIX}/usr") |
312 |
+# $(use_with X x "${EPREFIX}/usr") |
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+# $(use_with X x) # there is no --with-x option |
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+ ) |
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+ |
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+ # http://www.ncbi.nlm.nih.gov/books/NBK7167/ |
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+ use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) |
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+ |
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+ # TODO |
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+ # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure |
321 |
+ # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 |
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+ |
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+ einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" |
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+ |
325 |
+# ECONF_SOURCE="src/build-system" \ |
326 |
+# econf \ |
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+ bash \ |
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+ ./src/build-system/configure \ |
329 |
+ --srcdir="${S}" \ |
330 |
+ --prefix="${EPREFIX}/usr" \ |
331 |
+ --libdir=/usr/lib64 \ |
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+ --with-flat-makefile \ |
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+ ${myconf[@]} || die |
334 |
+#--without-debug \ |
335 |
+# --with-bin-release \ |
336 |
+# --with-bincopy \ |
337 |
+# --without-static \ |
338 |
+# --with-dll \ |
339 |
+# --with-mt \ |
340 |
+# --with-openmp \ |
341 |
+# --with-lfs \ |
342 |
+# --prefix="${ED}"/usr \ |
343 |
+# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ |
344 |
+# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ |
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+# || die |
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+# econf ${myconf[@]} |
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+} |
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+ |
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+src_compile() { |
350 |
+ ## all_r would ignore the --with-projects contents and build more |
351 |
+ ## emake all_r -C GCC*-Release*/build || die |
352 |
+ ## all_p with compile only selected/required components |
353 |
+ ##cd "${S}"_build &&\ |
354 |
+ ##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?" |
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+ #emake all_p -C "${S}"_build/build |
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+ |
357 |
+ # |
358 |
+ # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' |
359 |
+ # |
360 |
+ # The next release should automatically address such underlinking, albeit |
361 |
+ # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to |
362 |
+ # add or extend more DLL_LIB settings, to which end you may find the |
363 |
+ # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ |
364 |
+ # helpful. For instance, |
365 |
+ # |
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+ # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html |
367 |
+ # |
368 |
+ # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set |
369 |
+ # |
370 |
+ # DLL_LIB = xncbi |
371 |
+ # |
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+ # (You can find the path to that makefile by examining |
373 |
+ # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) |
374 |
+ # |
375 |
+ # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: |
376 |
+ emake -C "${S}"_build/build -f Makefile.flat |
377 |
+ # |
378 |
+ # >=gcc-5.3.0 is not supported, see also bug #579248#c8 |
379 |
+ # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 |
380 |
+} |
381 |
+ |
382 |
+src_install() { |
383 |
+ rm -rvf "${S}"_build/lib/ncbi || die |
384 |
+ emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" |
385 |
+ |
386 |
+# dobin "${S}"_build/bin/* |
387 |
+# dolib.so "${S}"_build/lib/*so* |
388 |
+# dolib.a "${S}"_build/lib/*.a |
389 |
+# doheader "${S}"_build/inc/* |
390 |
+ |
391 |
+ # File collisions with sci-biology/ncbi-tools |
392 |
+ mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ |
393 |
+ mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ |
394 |
+ mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries |
395 |
+ mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ |
396 |
+ mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ |
397 |
+ # |
398 |
+ # idfetch collides with idfetch from ncbi-tools-2.2.26 |
399 |
+ # Although the two idfetch implementations do deliberately have several |
400 |
+ # options in common, the C++ version is not yet a full drop-in replacement |
401 |
+ # for the C version (and will never entirely be, due to fundamental |
402 |
+ # differences between the two toolkits' argument-parsing conventions). |
403 |
+ mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0 |
404 |
+ |
405 |
+ echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} |
406 |
+ doenvd "${S}/99${PN}" |
407 |
+} |
408 |
+ |
409 |
+pkg_postinst() { |
410 |
+ einfo 'Please run "source /etc/profile" before using this package in the current shell.' |
411 |
+ einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' |
412 |
+} |