From: "Andrew Ammerlaan" <andrewammerlaan@riseup.net>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
Date: Tue, 5 Jan 2021 18:22:15 +0000 (UTC) [thread overview]
Message-ID: <1609870914.704db64ed869a89a3b0df65fb1e183816604b075.andrewammerlaan@gentoo> (raw)
commit: 704db64ed869a89a3b0df65fb1e183816604b075
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 5 10:05:05 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 5 18:21:54 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=704db64e
sci-biology/ncbi-tools++: depend on gcc<10, bump py targets
Closes: https://github.com/gentoo/sci/pull/1014
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 32 ++++++------
.../ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 60 +++++++++++-----------
.../ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 12 +++--
3 files changed, 55 insertions(+), 49 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 68341a338..0aa05e878 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
PYTHON_COMPAT=( python2_7 )
@@ -38,6 +38,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# sys-libs/db should be compiled with USE=cxx
# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
DEPEND="
+ <sys-devel/gcc-10:=
!sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:4.3[cxx] )
@@ -83,7 +84,21 @@ RDEPEND="${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
+ )
+
src_prepare() {
+ default
# filter-ldflags -Wl,--as-needed
# append-ldflags -Wl,--no-undefined
# sed -i -e 's/-print-file-name=libstdc++.a//' \
@@ -110,24 +125,11 @@ src_prepare() {
# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
- local PATCHES=(
- "${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}"/${P}-as-needed.patch
# "${FILESDIR}"/${P}-fix-creaders-linking.patch
# "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch
# )
# "${FILESDIR}"/${P}-support-autoconf-2.60.patch
- epatch ${PATCHES[@]}
# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
# https://bugs.gentoo.org/show_bug.cgi?id=514706
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index c737392fd..c3014adca 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
PYTHON_COMPAT=( python2_7 )
@@ -30,13 +30,14 @@ IUSE="
berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# sys-libs/db should be compiled with USE=cxx
# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
DEPEND="
+ <sys-devel/gcc-10:=
!sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:4.3[cxx] )
@@ -82,7 +83,34 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}/${MY_P}"
+PATCHES=(
+ "${FILESDIR}"/${P}-configure.patch
+ "${FILESDIR}"/${P}-fix-install.patch
+ "${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}"/${P}-fix-app-blast_sample-linking.patch
+ )
+
src_prepare() {
+ default
# filter-ldflags -Wl,--as-needed
# append-ldflags -Wl,--no-undefined
# sed -i -e 's/-print-file-name=libstdc++.a//' \
@@ -109,33 +137,7 @@ src_prepare() {
# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers
- local PATCHES=(
- "${FILESDIR}"/${P}-configure.patch
- "${FILESDIR}"/${P}-fix-install.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
- )
#ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch
- epatch ${PATCHES[@]}
# make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60
# https://bugs.gentoo.org/show_bug.cgi?id=514706
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 0c0e1b24c..ffa36ad4d 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
@@ -30,13 +30,14 @@ IUSE="
berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
sablotron sqlite tiff xerces xalan xml xpm xslt X"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# sys-libs/db should be compiled with USE=cxx
# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
DEPEND="
+ <sys-devel/gcc-10:=
!sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:4.3[cxx] )
@@ -83,6 +84,7 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}/${MY_P}"
src_prepare() {
+ default
# filter-ldflags -Wl,--as-needed
# append-ldflags -Wl,--no-undefined
# sed -i -e 's/-print-file-name=libstdc++.a//' \
@@ -254,7 +256,7 @@ src_configure() {
$(use_with mesa mesa "${EPREFIX}/usr")
$(use_with opengl glut "${EPREFIX}/usr")
$(use_with opengl glew "${EPREFIX}/usr")
- $(use_with opengl glew-mx)
+# $(use_with opengl glew-mx) can't find this with any version of media-libs/glew installed: explicitly specified, but no usable version found.
$(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
$(use_with wxwidgets wxwidgets-ucs)
$(use_with freetype freetype "${EPREFIX}/usr")
next reply other threads:[~2021-01-05 18:22 UTC|newest]
Thread overview: 49+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-01-05 18:22 Andrew Ammerlaan [this message]
-- strict thread matches above, loose matches on Subject: below --
2022-01-25 19:15 [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/ Andrew Ammerlaan
2021-08-31 9:45 Andrew Ammerlaan
2021-07-03 10:44 Andrew Ammerlaan
2021-03-16 18:49 Andrew Ammerlaan
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2021-01-10 19:09 Andrew Ammerlaan
2019-03-30 6:42 Martin Mokrejs
2019-03-30 0:13 Martin Mokrejs
2017-04-11 8:41 Martin Mokrejs
2017-03-27 5:35 Martin Mokrejs
2017-03-14 23:08 Martin Mokrejs
2016-12-03 11:34 Martin Mokrejs
2016-08-23 20:17 Justin Lecher
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2016-01-06 8:49 Justin Lecher
2015-07-17 0:40 Andrew Savchenko
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2013-09-13 20:23 Martin Mokrejs
2013-09-13 20:21 Martin Mokrejs
2013-06-12 20:07 Justin Lecher
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