From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 6367A1382C5 for ; Tue, 16 Mar 2021 18:49:48 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id A9C5AE07F9; Tue, 16 Mar 2021 18:49:47 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 7DAB0E07F9 for ; Tue, 16 Mar 2021 18:49:47 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 71967340E56 for ; Tue, 16 Mar 2021 18:49:46 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id CF0C8CC for ; Tue, 16 Mar 2021 18:49:44 +0000 (UTC) From: "Andrew Ammerlaan" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" Message-ID: <1615920392.6ae264536af8017178293a0f35242f4dfcd9e453.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild X-VCS-Directories: sci-biology/ncbi-tools++/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: 6ae264536af8017178293a0f35242f4dfcd9e453 X-VCS-Branch: master Date: Tue, 16 Mar 2021 18:49:44 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 39fa3cac-781c-4b1e-9c30-85cdd64af675 X-Archives-Hash: 26889648df1eea9dd13330ea500de49a commit: 6ae264536af8017178293a0f35242f4dfcd9e453 Author: Andrew Ammerlaan riseup net> AuthorDate: Tue Mar 16 18:46:32 2021 +0000 Commit: Andrew Ammerlaan riseup 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 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