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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2014-06-25 17:00:13 +0200
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2014-06-25 17:00:13 +0200
commit10e04f5023b0d6d66f63f277104707e2aea0fda7 (patch)
tree6b967afeb4874faa0c30d26bec84473c1cb65dc6 /sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
parentsci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ deps (diff)
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more changes to get ncbi-tools++-12.0.0 compiled
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.ebuild46
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() {