commit: a38e0d15267bbbe41f2e36f421c71b320d1c8326
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 17 18:27:57 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 17 18:27:57 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a38e0d15
sci-biology/ncbi-tools++: version bump, does not link yet
Package-Manager: Portage-2.3.3, Repoman-2.3.1
.../files/ncbi-tools++-18.0.0-configure.patch | 20 ++
.../files/ncbi-tools++-18.0.0-fix-install.patch | 11 +
...cbi-tools++-18.0.0-never_build_test_boost.patch | 11 +
.../ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 353 +++++++++++++++++++++
4 files changed, 395 insertions(+)
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch
new file mode 100644
index 000000000..b2d887c92
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch
@@ -0,0 +1,20 @@
+--- ncbi_cxx--12_0_0/src/build-system/configure.ori 2014-06-25
23:47:05.000000000 +0200
++++ ncbi_cxx--12_0_0/src/build-system/configure 2014-06-25
23:52:35.000000000 +0200
+@@ -3201,6 +3203,17 @@
+ *\ -O* | *\ -xO* ) skip_fast_flags=yes ;;
+ esac
+ fi
++if test -n "$with_projects"; then
++ case "$with_projects" in
++ /* ) abs_projects=$with_projects ;;
++ yes) abs_projects=$srcdir/projects ;;
++ * ) abs_projects=$srcdir/$with_projects ;;
++ esac
++ test -r "$abs_projects" || \
++ { { echo "$as_me:$LINENO: error: unable to read requested projects file
\"$abs_projects\"." >&5
++echo "$as_me: error: unable to read requested projects file
\"$abs_projects\"." >&2;}
++ { (exit 1); exit 1; }; }
++fi
+
+ #### Always define this
+
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch
new file mode 100644
index 000000000..97e845fdb
--- /dev/null
+++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori 2014-06-26
22:49:49.000000000 +0200
++++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top 2014-06-26
22:50:57.000000000 +0200
+@@ -48,7 +48,7 @@
+ for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done
+ cd $(includedir0) && find * -name CVS -prune -o -print |\
+ cpio -pd $(pincludedir)
+- $(INSTALL) -m 644 $(incdir)/* $(pincludedir)
++ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir)
+ ## set up appropriate build and status directories somewhere under $(libdir)?
+
+ install-gbench:
diff --git
a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch
new file mode 100644
index 000000000..68baea046
--- /dev/null
+++
b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch
@@ -0,0 +1,11 @@
+--- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori 2016-12-01
20:28:33.239758102 +0100
++++ ncbi_cxx--12_0_0/src/corelib/Makefile.in 2016-12-01 20:28:46.330110659
+0100
+@@ -7,7 +7,7 @@
+ #################################
+
+ USR_PROJ = precompile
+-LIB_PROJ = corelib test_mt test_boost
++LIB_PROJ = corelib test_mt
+ SUB_PROJ = test
+ PROJ_TAG = core
+
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
new file mode 100644
index 000000000..72f3ad016
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -0,0 +1,353 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+
+MY_TAG="Jun_15_2010"
+MY_Y="${MY_TAG/*_/}"
+MY_PV="18_0_0"
+MY_P="ncbi_cxx--${MY_PV}"
+#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
+
+# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
+DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit";
+SRC_URI="
+
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz";
+# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz";
+
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and
http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
+LICENSE="public-domain"
+SLOT="0"
+IUSE="
+ debug static-libs static threads pch
+ test wxwidgets odbc
+ berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+ glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+ sablotron sqlite tiff xerces xalan xml xpm xslt X"
+#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# sys-libs/db should be compiled with USE=cxx
+DEPEND="
+ !sci-biology/sra_sdk
+ app-arch/cpio
+ berkdb? ( sys-libs/db:4.3[cxx] )
+ boost? ( dev-libs/boost )
+ curl? ( net-misc/curl )
+ sqlite? ( dev-db/sqlite:3 )
+ mysql? ( virtual/mysql )
+ fltk? ( x11-libs/fltk )
+ opengl? ( virtual/opengl media-libs/glew:0= )
+ mesa? ( media-libs/mesa[osmesa] )
+ glut? ( media-libs/freeglut )
+ freetype? ( media-libs/freetype )
+ gnutls? ( net-libs/gnutls )
+ python? ( ${PYTHON_DEPS} )
+ cppunit? ( dev-util/cppunit )
+ icu? ( dev-libs/icu )
+ expat? ( dev-libs/expat )
+ sablotron? ( app-text/sablotron )
+ xml? ( dev-libs/libxml2 )
+ xslt? ( dev-libs/libxslt )
+ xerces? ( dev-libs/xerces-c )
+ xalan? ( dev-libs/xalan-c )
+ muparser? ( dev-cpp/muParser )
+ hdf5? ( sci-libs/hdf5[cxx] )
+ gif? ( media-libs/giflib )
+ jpeg? ( virtual/jpeg:0= )
+ png? ( media-libs/libpng:0= )
+ tiff? ( media-libs/tiff:0= )
+ xpm? ( x11-libs/libXpm )
+ dev-libs/lzo
+ app-arch/bzip2
+ dev-libs/libpcre"
+# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC
OEChem sge
+# Intentionally omitted USE flags:
+# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is
currently broken.
+# The default (heavily patched) embedded copy
should work, or you can
+# leave it off altogether -- the only public apps
that make use of it are
+# samples and tests, since NCBI's database
servers are of course firewalled.
+
+# seems muParser is required, also glew is required. configure exits otherwise
if these are explicitly passed to it (due to USE flag enabled)
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+# filter-ldflags -Wl,--as-needed
+# append-ldflags -Wl,--no-undefined
+# sed -i -e 's/-print-file-name=libstdc++.a//' \
+# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
+# src/build-system/configure || die
+# epatch \
+# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
+# "${FILESDIR}"/curl-types.patch \
+# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \
+# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
+# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \
+# "${FILESDIR}"/report_project_settings_configure.ac.patch \
+# "${FILESDIR}"/report_project_settings_configure.patch \
+# "${FILESDIR}"/make_install.patch
+
+# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
+
+# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
+# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
+# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
+# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
+# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
+
+# use prefix && append-ldflags
-Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
+
+# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line
numbers
+ local PATCHES=(
+ "${FILESDIR}"/${P}-configure.patch
+ "${FILESDIR}"/${P}-fix-install.patch
+ "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
+ )
+ epatch ${PATCHES[@]}
+ # make sure this one is the last one and contains the actual patches
applied unless we can have autoconf-2.59 or 2.60
+ # https://bugs.gentoo.org/show_bug.cgi?id=514706
+
+ tc-export CXX CC
+
+ cd src/build-system || die
+# eautoreconf
+
+ # Temporarily disabling eautoconf because we patch configure via
${P}-support-autoconf-2.60.patch
+ # eautoconf # keep it disabled until we can ensure 2.59 is installed
+ # beware 12.0.0. and previous required autoconf-2.59, a patch for
12.0.0 brings autoconf-2.60 support
+}
+
+# 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
+src_configure() {
+ local myconf=()
+ #--without-optimization turn off optimization flags in non-debug mode
+ #--with-profiling build profiled versions of libs and apps
+ #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR)
+ #--with-plugin-auto-load always enable the plugin manager by default
+ #--with-bundles build bundles in addition to dylibs on Mac OS X
+ #--with-bin-release build executables suitable for public release
+ # no dll and such
+ #--with-64 compile to 64-bit code
+ #--with-universal build universal binaries on Mac OS X
+ #--with-universal=CPUs build universal binaries targeting the given
CPUs
+ #--without-exe do not build executables
+ #--with-relative-runpath=P specify an executable-relative DLL search
path
+ #--with-hard-runpath hard-code runtime path, ignoring
LD_LIBRARY_PATH
+ #--with-limited-linker don't attempt to build especially large
projects
+ #--with-extra-action= script to call after the configuration is
complete
+ #--with-autodep automatic generation of dependencies (GNU make)
+ #--with-fake-root=DIR appear to have been built under DIR
+ #--with-build-root-sfx=X add a user-specified suffix to the build dir
name
+ #--without-execopy do not copy built executables to the BIN area
+ #--with-lib-rebuilds ensure that apps use up-to-date libraries
+ #--with-lib-rebuilds=ask ask whether to update each app's libraries
+ #--without-deactivation keep old copies of libraries that no longer
build
+ #--without-makefile-auto-update do not auto-update generated makefiles
+ #--with-projects=FILE build projects listed in FILE by default
+ #--without-flat-makefile do not generate an all-encompassing flat
makefile
+ #--with-configure-dialog allow interactive flat makefile project
selection
+ #--with-saved-settings=F load configuration settings from the file F
+ #--with-check-tools=... use the specified tools for testing
+ #--with-ncbi-public ensure compatibility for all in-house platforms
+ #--with-sybase-local=DIR use local SYBASE install (DIR is optional)
+ #--with-sybase-new use newer SYBASE install (12.5 rather than
12.0)
+ #--without-sp do not use SP libraries
+ #--without-orbacus do not use ORBacus CORBA libraries
+ #--with-orbacus=DIR use ORBacus installation in DIR
+ #--with-jni(=JDK-DIR) build Java bindings (against the JDK in
JDK-DIR)
+ #--with-sablot=DIR use Sablotron installation in DIR
+ #--without-sablot, do not use Sablotron
+ #--with-oechem=DIR use OpenEye OEChem installation in DIR
+ #--without-oechem do not use OEChem
+ #--with-sge=DIR use Sun Grid Engine installation in DIR
+ #--without-sge do not use Sun Grid Engine
+ #--with-magic=DIR use libmagic installation in DIR
+ #--without-magic do not use libmagic
+ #--without-local-lbsm turn off support for IPC with locally running
LBSMD
+ #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt
+ #--without-connext do not build non-public CONNECT library
extensions
+ #--without-serial do not build the serialization library and
tools
+ #--without-objects do not generate/build serializeable objects
from ASNs
+ #--without-dbapi do not build database connectivity libraries
+ #--without-app do not build standalone applications like
ID1_FETCH
+ #--without-gui do not build most graphical projects
+ #--without-algo do not build CPU-intensive algorithms
+ #--without-internal do not build internal projects
+ #--with-gbench ensure that Genome Workbench can be built
+ #--without-gbench do not build Genome Workbench
+ myconf+=(
+ --with-dll
+ --with-lfs
+ --with-build-root="${S}"_build
+ --without-suffix
+ --without-hostspec
+ --without-version
+ --with-bincopy
+ --without-strip
+ --without-ccache
+ --without-distcc
+# --with-ncbi-c
+ --without-ctools
+# --with-sss
+# --with-sssutils
+# --with-sssdb
+# --with-included-sss
+ --with-z="${EPREFIX}/usr"
+ --with-bz2="${EPREFIX}/usr"
+ --without-sybase
+ --with-autodep
+# --with-3psw=std:netopt favor standard (system) builds of the above pkgs
+ # --without-downloaded-vdb is not available in 12.0.0 release yet
+ # 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)
+ $(use_with static-libs static)
+ $(use_with static static-exe)
+ $(use_with threads mt)
+ $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}")
+ $(use_with test check)
+ $(use_with pch)
+ $(use_with lzo lzo "${EPREFIX}/usr")
+ $(use_with pcre pcre "${EPREFIX}/usr")
+ $(use_with gnutls gnutls "${EPREFIX}/usr")
+ $(use_with mysql mysql "${EPREFIX}/usr")
+ $(use_with muparser muparser "${EPREFIX}/usr")
+ $(usex fltk --with-fltk="${EPREFIX}/usr" "")
+ $(use_with opengl opengl "${EPREFIX}/usr")
+ $(use_with mesa mesa "${EPREFIX}/usr")
+ $(use_with opengl glut "${EPREFIX}/usr")
+ $(use_with opengl glew "${EPREFIX}/usr")
+ $(use_with opengl glew-mx)
+ $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
+ $(use_with wxwidgets wxwidgets-ucs)
+ $(use_with freetype freetype "${EPREFIX}/usr")
+ $(use_with fastcgi fastcgi "${EPREFIX}/usr")
+ $(use_with berkdb bdb "${EPREFIX}/usr")
+ $(usex odbc --with-odbc="${EPREFIX}/usr" "")
+ $(use_with python python "${EPREFIX}/usr")
+ $(use_with boost boost "${EPREFIX}/usr")
+ $(use_with sqlite sqlite3 "${EPREFIX}/usr")
+ $(use_with icu icu "${EPREFIX}/usr")
+ $(use_with expat expat "${EPREFIX}/usr")
+ $(use_with xml libxml "${EPREFIX}/usr")
+ $(use_with xml libxslt "${EPREFIX}/usr")
+ $(use_with xerces xerces "${EPREFIX}/usr")
+ $(use_with hdf5 hdf5 "${EPREFIX}/usr")
+ $(use_with xalan xalan "${EPREFIX}/usr")
+# $(use_with gif gif "${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"
+ --without-gif
+ $(use_with jpeg jpeg "${EPREFIX}/usr")
+ $(use_with tiff tiff "${EPREFIX}/usr")
+ $(use_with png png "${EPREFIX}/usr")
+ $(use_with xpm xpm "${EPREFIX}/usr")
+ $(use_with curl curl "${EPREFIX}/usr")
+# $(use_with X x "${EPREFIX}/usr")
+# $(use_with X x) # there is no --with-x option
+ )
+
+ # http://www.ncbi.nlm.nih.gov/books/NBK7167/
+ use test || myconf+=(
--with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
+
+ # TODO
+ # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass
that also to configure
+ # otherwise your -O2 will be dropped in some subdirectories and
replaced by e.g. -O9
+
+ einfo "bash ./src/build-system/configure --srcdir="${S}"
--prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
+
+# ECONF_SOURCE="src/build-system" \
+# econf \
+ bash \
+ ./src/build-system/configure \
+ --srcdir="${S}" \
+ --prefix="${EPREFIX}/usr" \
+ --libdir=/usr/lib64 \
+ --with-flat-makefile \
+ ${myconf[@]} || die
+#--without-debug \
+# --with-bin-release \
+# --with-bincopy \
+# --without-static \
+# --with-dll \
+# --with-mt \
+# --with-openmp \
+# --with-lfs \
+# --prefix="${ED}"/usr \
+# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
+# ${myconf} LDFLAGS="-Wl,--no-as-needed" \
+# || die
+# econf ${myconf[@]}
+}
+
+src_compile() {
+ ## all_r would ignore the --with-projects contents and build more
+ ## emake all_r -C GCC*-Release*/build || die
+ ## all_p with compile only selected/required components
+ ##cd "${S}"_build &&\
+ ##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?"
+ #emake all_p -C "${S}"_build/build
+
+ #
+ # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference
to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)'
+ #
+ # The next release should automatically address such underlinking,
albeit
+ # only in --with-flat-makefile configurations. For now (12.0.0),
you'll need to
+ # add or extend more DLL_LIB settings, to which end you may find the
+ # resources at
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/
+ # helpful. For instance,
+ #
+ #
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html
+ #
+ # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set
+ #
+ # DLL_LIB = xncbi
+ #
+ # (You can find the path to that makefile by examining
+ # .../status/.dbapi_driver.dep or .../build/Makefile.flat.)
+ #
+ # To take full advantage of --with-flat-makefile, you'll need the
following (instead of 'emake all_p -C "${S}"_build/build') and call configure
--with-flat-makefile:
+ emake -C "${S}"_build/build -f Makefile.flat
+ #
+ # >=gcc-5.3.0 is not supported, see also bug #579248#c8
+ # configure: error: Do not know how to build MT-safe with compiler
/usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0
+}
+
+src_install() {
+ rm -rvf "${S}"_build/lib/ncbi || die
+ emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
+
+# dobin "${S}"_build/bin/*
+# dolib.so "${S}"_build/lib/*so*
+# dolib.a "${S}"_build/lib/*.a
+# doheader "${S}"_build/inc/*
+
+ # File collisions with sci-biology/ncbi-tools
+ mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+
+ mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+
+ mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop
the eventually mistakenly compiled binaries
+ mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+
+ mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+
+
+ echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
+ doenvd "${S}/99${PN}"
+}
+
+pkg_postinst() {
+ einfo 'Please run "source /etc/profile" before using this package in
the current shell.'
+ einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
+}
