diff options
Diffstat (limited to 'sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild')
| -rw-r--r-- | sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 46 |
1 files changed, 36 insertions, 10 deletions
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 2a77c11d2..ecb94f0f8 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -112,9 +112,12 @@ src_prepare() { "${FILESDIR}"/${P}-fix-creaders-linking.patch "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch - "${FILESDIR}"/${P}-support-autoconf-2.60.patch - "${FILESDIR}"/${P}-configure.patch + "${FILESDIR}"/${P}-more-patches.patch + "${FILESDIR}"/${P}-linking.patch + "${FILESDIR}"/${P}-linking2.patch ) + # "${FILESDIR}"/${P}-support-autoconf-2.60.patch + # "${FILESDIR}"/${P}-configure.patch 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 @@ -248,7 +251,8 @@ src_configure() { $(use_with xerces xerces "${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") # 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") @@ -263,7 +267,7 @@ src_configure() { # 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 repalced by e.g. -O9 + # 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 ${myconf[@]}" @@ -274,6 +278,7 @@ src_configure() { --srcdir="${S}" \ --prefix="${EPREFIX}/usr" \ --libdir=/usr/lib64 \ + --with-flat-makefile \ ${myconf[@]} || die #--without-debug \ # --with-bin-release \ @@ -291,12 +296,33 @@ src_configure() { } src_compile() { - # all_r would ignore the --with-projects contents and build more - # emake all_r -C GCC*-Release*/build || die - # all_p with compile only selected/required components -# cd "${S}"_build &&\ - emake all_p -C "${S}"_build/build -# emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" + ## all_r would ignore the --with-projects contents and build more + ## emake all_r -C GCC*-Release*/build || die + ## all_p with compile only selected/required components + ##cd "${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 } src_install() { |