commit: 6ae264536af8017178293a0f35242f4dfcd9e453
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Mar 16 18:46:32 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Mar 16 18:46:32 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ae26453
Revert "sci-biology/ncbi-tools++: drop py2 only version"
This reverts commit e8d4a8bc048182c0db34a3b995ac6a5c24fcdbb8.
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
...++-18.0.0.ebuild => ncbi-tools++-12.0.0.ebuild} | 51 ++++++++--------------
.../ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 2 +-
2 files changed, 19 insertions(+), 34 deletions(-)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
similarity index 89%
copy from sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
copy to sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 5c0b619df..ed50801fc 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -3,13 +3,13 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
MY_TAG="Jun_15_2010"
MY_Y="${MY_TAG/*_/}"
-MY_PV="18_0_0"
+MY_PV="12_0_0"
MY_P="ncbi_cxx--${MY_PV}"
#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
@@ -17,7 +17,7 @@ MY_P="ncbi_cxx--${MY_PV}"
DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
HOMEPAGE="https://ncbi.github.io/cxx-toolkit/";
SRC_URI="
-
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz";
+
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${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
@@ -30,7 +30,8 @@ IUSE="
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"
+#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64"
RESTRICT="!test? ( test )"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
@@ -85,29 +86,16 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}/${MY_P}"
PATCHES=(
+ "${FILESDIR}"/${P}-conf-opts.patch
+ "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
+ "${FILESDIR}"/${P}-linkage-tuneups.patch
+ "${FILESDIR}"/${P}-more-patches.patch
+ "${FILESDIR}"/${P}-linkage-tuneups-addons.patch
"${FILESDIR}"/${P}-configure.patch
+ "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch
"${FILESDIR}"/${P}-fix-install.patch
+ "${FILESDIR}"/${P}-bdb6.patch
"${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248
- "${FILESDIR}"/${P}-fix-annotwriter-linking.patch
- "${FILESDIR}"/${P}-fix-undefined-xobjread.patch
- "${FILESDIR}"/${P}-fix-apps-blast-linking.patch
- "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch
- "${FILESDIR}"/${P}-fix-app-compartp-linking.patch
- "${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch
- "${FILESDIR}"/${P}-fix-app-hfilter-linking.patch
- "${FILESDIR}"/${P}-fix-app-igblast-linking.patch
- "${FILESDIR}"/${P}-fix-ncfetch-linking.patch
- "${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch
- "${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch
- "${FILESDIR}"/${P}-fix-speedtest-linking.patch
- "${FILESDIR}"/${P}-fix-splign-linking.patch
- "${FILESDIR}"/${P}-fix-srcchk-linking.patch
- "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch
- "${FILESDIR}"/${P}-remove-old-symlinks.patch
- "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch
- "${FILESDIR}"/${P}-fix-app-tls-linking.patch
- "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch
- "${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch
)
src_prepare() {
@@ -138,7 +126,11 @@ src_prepare() {
# use prefix && append-ldflags
-Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line
numbers
- #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
+# "${FILESDIR}"/${P}-as-needed.patch
+# "${FILESDIR}"/${P}-fix-creaders-linking.patch
+# "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
+# )
+ # "${FILESDIR}"/${P}-support-autoconf-2.60.patch
# 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
@@ -237,7 +229,7 @@ src_configure() {
# resulting in 'checking for ncbi-vdb... no' and
# '^PACKAGES:'
# '^ disabled: ... VDB'
- --without-downloaded-vdb
+ # --without-downloaded-vdb
$(use_with debug)
$(use_with debug max-debug)
$(use_with debug symbols)
@@ -366,13 +358,6 @@ src_install() {
mv -f "${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 "${ED}"/usr/bin/seedtop+
- #
- # idfetch collides with idfetch from ncbi-tools-2.2.26
- # Although the two idfetch implementations do deliberately have several
- # options in common, the C++ version is not yet a full drop-in
replacement
- # for the C version (and will never entirely be, due to fundamental
- # differences between the two toolkits' argument-parsing conventions).
- mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in
ncbi-tools++-18.0.0
echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
doenvd "${S}/99${PN}"
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 5c0b619df..0aacd0511 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7,8,9} )
+PYTHON_COMPAT=( python2_7 )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
