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 TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 1BADE158093 for ; Sat, 2 Jul 2022 22:33:37 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 52FECE0B33; Sat, 2 Jul 2022 22:33:36 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 36143E0B33 for ; Sat, 2 Jul 2022 22:33:36 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 11DF7341C02 for ; Sat, 2 Jul 2022 22:33:35 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 91F04326 for ; Sat, 2 Jul 2022 22:33:33 +0000 (UTC) From: "Sam James" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Sam James" Message-ID: <1656801191.4e3464f740a62b786296d21274e6197b8f3a4bd0.sam@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/vcftools/, sci-biology/vcftools/files/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/vcftools/Manifest sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch sci-biology/vcftools/vcftools-0.1.14.ebuild X-VCS-Directories: sci-biology/vcftools/files/ sci-biology/vcftools/ X-VCS-Committer: sam X-VCS-Committer-Name: Sam James X-VCS-Revision: 4e3464f740a62b786296d21274e6197b8f3a4bd0 X-VCS-Branch: master Date: Sat, 2 Jul 2022 22:33:33 +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: 32fcc51a-8a18-49cf-b5af-0c6b8925f9e1 X-Archives-Hash: 5ab735c05b9900eadf67e8c2f1313b66 commit: 4e3464f740a62b786296d21274e6197b8f3a4bd0 Author: Sam James gentoo org> AuthorDate: Sat Jul 2 22:33:11 2022 +0000 Commit: Sam James gentoo org> CommitDate: Sat Jul 2 22:33:11 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4e3464f7 sci-biology/vcftools: drop 0.1.14 Signed-off-by: Sam James gentoo.org> sci-biology/vcftools/Manifest | 1 - .../files/vcftools-0.1.14-buildsystem.patch | 50 ---------------------- sci-biology/vcftools/vcftools-0.1.14.ebuild | 39 ----------------- 3 files changed, 90 deletions(-) diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest index 411610b28376..36aa8e465e22 100644 --- a/sci-biology/vcftools/Manifest +++ b/sci-biology/vcftools/Manifest @@ -1,2 +1 @@ -DIST vcftools-0.1.14.tar.gz 342369 BLAKE2B 14be867c0be41767e2c97c8be212f3cff495c1cb6699294fb8a26ac491901599cd1e400cb80c6d609dce36584ee5defdb3b3652657bd127e0c67c5b29a842cc5 SHA512 863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7 DIST vcftools-0.1.16.tar.gz 480575 BLAKE2B 5c0bf67aef8ef4705f621485df4c556f6bace190311c308f0364f3e274cf4818f56f2186905fdfb7459dc4be9664a8b1ff631e2cecd03abd7aa82dcfc7e5aa64 SHA512 c4dd5ceb3ad0512e839154d8a05ef3e7a03cbe52c3099df48775b35460fce7ef10102819c2d1cefa33b98ad09e7bd1608e871978860ec9c0b0c2e781892b22e6 diff --git a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch deleted file mode 100644 index 126a709385db..000000000000 --- a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch +++ /dev/null @@ -1,50 +0,0 @@ -* Add prefix in Makefiles, not the configure script -* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB, - as it is more flexible and helps us with LAPACK -* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS - ---- a/configure.ac -+++ b/configure.ac -@@ -34,7 +34,7 @@ - [--with-pmdir=DIR], - [install Perl modules in DIR]), - [PMDIR=${withval}], -- [PMDIR='${prefix}'/"$pmdir_relative_path"]) -+ [PMDIR="$pmdir_relative_path"]) - - AC_SUBST([PMDIR]) - -@@ -73,9 +73,9 @@ - [pca=${enableval}], - [pca=no]) - --if test "x${pca}" = "xyes" ; then -- AC_CHECK_LIB(lapack, dgeev_) --fi -+AS_IF([test "x${pca}" = "xyes"],[ -+ AC_SEARCH_LIBS([dgeev_], [lapack]) -+]) - - # Generate output. - AC_CONFIG_FILES([Makefile ---- a/src/cpp/Makefile.am -+++ b/src/cpp/Makefile.am -@@ -1,6 +1,6 @@ - bin_PROGRAMS = vcftools - --vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS) -+vcftools_CPPFLAGS = $(ZLIB_CFLAGS) - vcftools_LDADD = $(ZLIB_LIBS) - - vcftools_SOURCES = \ ---- a/src/perl/Makefile.am -+++ b/src/perl/Makefile.am -@@ -24,7 +24,7 @@ - vcf-tstv \ - vcf-validator - --pmdir = $(PMDIR) -+pmdir = $(exec_prefix)/$(PMDIR) - - dist_pm_DATA = \ - FaSlice.pm \ diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.14.ebuild deleted file mode 100644 index 7b386453ae25..000000000000 --- a/sci-biology/vcftools/vcftools-0.1.14.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools flag-o-matic perl-functions toolchain-funcs - -DESCRIPTION="Tools for working with VCF (Variant Call Format) files" -HOMEPAGE="http://vcftools.sourceforge.net/" -SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="lapack" - -RDEPEND="sys-libs/zlib - dev-lang/perl:= - lapack? ( virtual/lapack )" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( "${FILESDIR}/${PN}-0.1.14-buildsystem.patch" ) - -src_prepare() { - default - eautoreconf -} - -src_configure() { - perl_set_version - - append-flags $($(tc-getPKG_CONFIG) --cflags lapack) - append-libs $($(tc-getPKG_CONFIG) --libs lapack) - - econf \ - $(use_enable lapack pca) \ - --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}" -}