diff options
Diffstat (limited to 'sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild')
| -rw-r--r-- | sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 188 |
1 files changed, 69 insertions, 119 deletions
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 index 9806b413d..439e91722 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -inherit eutils flag-o-matic multilib toolchain-funcs +inherit autotools eutils flag-o-matic multilib toolchain-funcs MY_TAG="Jun_15_2010" MY_Y="${MY_TAG/*_/}" @@ -68,70 +68,6 @@ DEPEND=" dev-libs/libpcre" # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# configure options, may want to expose some -# --without-debug build non-debug versions of libs and apps -# --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-dll build all libraries as DLLs -# --with-static build all libraries statically even if --with-dll -# --with-static-exe build all executables as statically as possible -# --with-plugin-auto-load always enable the plugin manager by default -# --with-bin-release build executables suitable for public release -# --with-mt compile in a MultiThread-safe manner -# --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-runpath= hard-code the runtime path to DLLs -# --with-lfs enable large file support to the extent possible -# --with-extra-action= script to call after the configuration is complete -# --with-autodep automatic generation of dependencies (GNU make) -# --with-build-root=DIR specify a non-default build directory name -# --with-fake-root=DIR appear to have been built under DIR -# --without-suffix no Release/Debug, MT or DLL sfx in the build dir name -# --with-hostspec add full host specs to the build dir name -# --without-version don't always include the cplr ver in the bd name -# --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-bincopy populate lib and bin with copies, not hard links -# --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 run test suite after the build -# --with-check-tools=... use the specified tools for testing -# --with-ncbi-public ensure compatibility for all in-house platforms -# --with-strip strip binaries at build time -# --with-pch use precompiled headers if possible -# --with-caution cancel configuration unconditionally when in doubt -# --without-caution proceed without asking when in doubt -# --without-ccache do not automatically use ccache if available -# --without-distcc do not automatically use distcc if available -# --without-ncbi-c do not use NCBI C Toolkit -# --without-sss do not use NCBI SSS libraries -# --without-utils do not use NCBI SSS UTIL library -# --without-sssdb do not use NCBI SSS DB library -# --with-included-sss use the in-tree copy of SSS - -# --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-ctools do not build NCBI C Toolkit based projects -# --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 - RDEPEND="${DEPEND}" S="${WORKDIR}/${MY_P}" @@ -162,7 +98,17 @@ src_prepare() { # "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch # use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" + + local PATCHES=( + "${FILESDIR}"/${P}-conf-opts.patch + "${FILESDIR}"/${P}-as-needed.patch + ) + epatch ${PATCHES[@]} + tc-export CXX CC +# cd src/build-system || die +# eaclocal -I. +# eautoconf } src_configure() { @@ -175,54 +121,54 @@ src_configure() { #--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-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-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-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 + #--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-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) + #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) #--without-ftds-renamed do not rename Sybase DBLIB symbols in built-in FTDS #--without-sp do not use SP libraries #--without-orbacus do not use ORBacus CORBA libraries - # --with-orbacus=DIR use ORBacus installation in DIR + #--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 + #--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 + #--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-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-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 + #--with-gbench ensure that Genome Workbench can be built + #--without-gbench do not build Genome Workbench myconf+=( --with-dll --with-lfs @@ -234,17 +180,18 @@ src_configure() { --without-strip --without-ccache --without-distcc - --with-ncbi-c +# --with-ncbi-c --without-ctools - --with-sss - --with-utils - --with-sssdb - --with-included-sss +# --with-sss +# --with-sssutils +# --with-sssdb +# --with-included-sss --with-z="${EPREFIX}"/usr --with-bz2="${EPREFIX}"/usr --with-muparser="${EPREFIX}"/usr --without-sybase -# --with-3psw=std:netopt + --with-autodep +# --with-3psw=std:netopt favor standard (system) builds of the above pkgs $(use_with debug) $(use_with debug max-debug) $(use_with debug symbols) @@ -265,7 +212,7 @@ src_configure() { $(use_with mesa mesa "${EPREFIX}"/usr) $(use_with opengl glut "${EPREFIX}"/usr) $(use_with opengl glew "${EPREFIX}"/usr) - $(use_with opengl glew-m) + $(use_with opengl glew-mx) $(use_with wxwidgets wxwidgets "${EPREFIX}"/usr) $(use_with wxwidgets wxwidgets-ucs) $(use_with freetype freetype "${EPREFIX}"/usr) @@ -277,18 +224,19 @@ src_configure() { $(use_with sqlite sqlite3 "${EPREFIX}"/usr) $(use_with icu icu "${EPREFIX}"/usr) $(use_with expat expat "${EPREFIX}"/usr) - $(use_with xml libxml2 "${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) +# $(use_with gif gif "${EPREFIX}"/usr) $(use_with jpeg jpeg "${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) +# $(use_with X x "${EPREFIX}"/usr) + $(use_with X x) ) # http://www.ncbi.nlm.nih.gov/books/NBK7167/ @@ -298,16 +246,16 @@ src_configure() { # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure # otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9 - "${S}"/configure \ - --prefix="${EPREFIX}"/usr \ - --build=x86_64-pc-linux-gnu \ - --host=x86_64-pc-linux-gnu \ - --infodir=/usr/share/info \ - --datadir=/usr/share \ - --sysconfdir=/etc \ - --localstatedir=/var/lib \ - --libdir=/usr/lib64 \ - ${myconf[@]} || die + einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}"/usr --libdir=/usr/lib64 ${myconf[@]}" + +# bash \ +# ./src/build-system/configure \ +# cd src/build-system || die + econf \ + --srcdir="${S}" \ + --prefix="${EPREFIX}"/usr \ + --libdir=/usr/lib64 \ + ${myconf[@]} || die #--without-debug \ # --with-bin-release \ # --with-bincopy \ @@ -326,7 +274,9 @@ src_compile() { # all_r would ignore the --with-projects contents and build more # emake all_r -C GCC*-Release*/build || die # all_p with compile only selected/required components - emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" +# cd "${S}"_build &&\ + emake all_p -C "${S}"_build/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?" } src_install() { |