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 | 33 |
1 files changed, 30 insertions, 3 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 8c190e48b..4e1ee2e3e 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 @@ -24,7 +24,7 @@ IUSE=" debug static-libs static threads pch test wxwidgets odbc berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python + glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X" #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" KEYWORDS="" @@ -42,7 +42,9 @@ DEPEND=" ssl? ( dev-libs/openssl ) fltk? ( x11-libs/fltk ) opengl? ( virtual/opengl ) - mesa? ( media-libs/mesa ) + mesa? ( media-libs/mesa + media-libs/glew + ) glut? ( media-libs/freeglut ) freetype? ( media-libs/freetype ) fastcgi? ( www-apache/mod_fastcgi ) @@ -67,6 +69,9 @@ DEPEND=" dev-libs/libpcre" # USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge + +# seems muParser is required, also glew is required. configure exitss otherwise + RDEPEND="${DEPEND}" S="${WORKDIR}/${MY_P}" @@ -100,6 +105,10 @@ src_prepare() { local PATCHES=( "${FILESDIR}"/${P}-conf-opts.patch "${FILESDIR}"/${P}-as-needed.patch + "${FILESDIR}"/${P}-fix-creaders-linking.patch + "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch + "${FILESDIR}"/${P}-fix-undef-reference-to-GenBankReaders_Register_Id1.patch + "${FILESDIR}"/${P}-remove-LZO-definition-upstream.patch ) epatch ${PATCHES[@]} @@ -190,7 +199,17 @@ src_configure() { --with-muparser="${EPREFIX}/usr" --without-sybase --with-autodep + +# due to \*-fix-undef-reference-to-GenBankReaders_Register_Id1.patch +# ./configure ... --with-flat-makefile +# cd .../build +# make -f Makefile.flat +# + --with-flat-makefile # --with-3psw=std:netopt favor standard (system) builds of the above pkgs + + +# TODO: should improve the ssl/openssl/gmutls logic like is in net-misc/vpnc $(use_with debug) $(use_with debug max-debug) $(use_with debug symbols) @@ -254,6 +273,7 @@ src_configure() { --srcdir="${S}" \ --prefix="${EPREFIX}/usr" \ --libdir=/usr/lib64 \ + ${myconf} LDFLAGS="-Wl,-rpath-link,${S}_build/lib -Wl,--no-as-needed" \ ${myconf[@]} || die #--without-debug \ # --with-bin-release \ @@ -274,7 +294,14 @@ src_compile() { # emake all_r -C GCC*-Release*/build || die # all_p with compile only selected/required components # cd "${S}"_build &&\ - emake all_p -C "${S}"_build/build + + # disabling this because we need to take the flat Makefile route + # emake all_p -C "${S}"_build/build + + # take the flat Makefile route + emake -f Makefile.flat -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?" } |