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 8E1D61382C5 for ; Tue, 1 May 2018 15:14:18 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 788A1E09B6; Tue, 1 May 2018 15:14:17 +0000 (UTC) Received: from smtp.gentoo.org (dev.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 3C808E09B6 for ; Tue, 1 May 2018 15:14:17 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (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 42F61335C78 for ; Tue, 1 May 2018 15:14:15 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 5BB082A5 for ; Tue, 1 May 2018 15:14:13 +0000 (UTC) From: "Marek Szuba" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Marek Szuba" Message-ID: <1525187633.0243d563e8de7d1eb26227665892172dbf3379f6.marecki@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: dev-perl/Bio-DB-HTS/, dev-perl/Bio-DB-HTS/files/ X-VCS-Repository: repo/gentoo X-VCS-Files: dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild dev-perl/Bio-DB-HTS/Manifest dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch X-VCS-Directories: dev-perl/Bio-DB-HTS/files/ dev-perl/Bio-DB-HTS/ X-VCS-Committer: marecki X-VCS-Committer-Name: Marek Szuba X-VCS-Revision: 0243d563e8de7d1eb26227665892172dbf3379f6 X-VCS-Branch: master Date: Tue, 1 May 2018 15:14:13 +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-Archives-Salt: 51b63ce2-0b32-4a7d-893f-2d474e0059d2 X-Archives-Hash: 72d0bda55ffd2c42d9d00d4ccc895b32 commit: 0243d563e8de7d1eb26227665892172dbf3379f6 Author: Marek Szuba gentoo org> AuthorDate: Tue May 1 13:48:24 2018 +0000 Commit: Marek Szuba gentoo org> CommitDate: Tue May 1 15:13:53 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0243d563 dev-perl/Bio-DB-HTS: remove old Package-Manager: Portage-2.3.24, Repoman-2.3.6 dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild | 32 --------------- dev-perl/Bio-DB-HTS/Manifest | 1 - .../files/2.10-build_search_for_so.patch | 29 ------------- .../files/2.10-build_split_htslib_opts.patch | 48 ---------------------- 4 files changed, 110 deletions(-) diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild deleted file mode 100644 index 0a150300213..00000000000 --- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -DIST_AUTHOR=AVULLO -DIST_VERSION=2.10 - -inherit perl-module - -DESCRIPTION="Perl bindings for sci-libs/htslib" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" - -RDEPEND="sci-biology/bioperl - sci-libs/htslib:=" -DEPEND="${RDEPEND} - dev-perl/Module-Build - test? ( dev-perl/Test-LeakTrace )" - -PATCHES=( - "${FILESDIR}/2.10-build_search_for_so.patch" - "${FILESDIR}/2.10-build_split_htslib_opts.patch" -) - -src_configure() { - local myconf="--htslib-includedir=${EPREFIX}/usr/include/htslib --htslib-libdir=${EPREFIX}/usr/$(get_libdir)" - perl-module_src_configure -} diff --git a/dev-perl/Bio-DB-HTS/Manifest b/dev-perl/Bio-DB-HTS/Manifest index 6770bf66986..3eaf22e7a99 100644 --- a/dev-perl/Bio-DB-HTS/Manifest +++ b/dev-perl/Bio-DB-HTS/Manifest @@ -1,2 +1 @@ -DIST Bio-DB-HTS-2.10.tar.gz 5245650 BLAKE2B a52d9b1e19d5920d61dd365eacfd1a40726500e25a3ab516df5a1d59a7a9d79ce02db7a2145801b6af5df2c41c95e80b49a39db83d27fd7ff3cf88ba0e6a328d SHA512 4e7c01022d9edf48a0e0dcffcbccf34812f236d1b581760ac115c323de5779fb6212eb4ad7d1953811930a6137cc8f5f59028c73d645d1ca5fb6118dd846ad57 DIST Bio-DB-HTS-2.11.tar.gz 5250814 BLAKE2B d77ccacebf339a33ab106b997139cdbf79f6c28269a832305e660b28370aca82b4c9824773acdbf8f59b18dd61f40346a9870578dba7b5b989b0f3bc9ad14b35 SHA512 114d90fe92b684250183b45b4d23d2dd45ecdcb2fa54f7b1c311ed668d8e87953adb861f709a0a48ff2b873ce777b21bc3b557bafa0df216b9a71b59facff6fd diff --git a/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch b/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch deleted file mode 100644 index b3d11bbbe7a..00000000000 --- a/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- a/Build.PL -+++ b/Build.PL -@@ -125,7 +125,7 @@ - - my $hts_lib = "$root"; - my $hts_include = "$root/htslib"; -- if (-f "$hts_lib/libhts.a" && -f "$hts_include/hts.h") { -+ if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") { - $self->config_data('hts_lib' => $hts_lib); - $self->config_data('hts_include' => $hts_include); - return 1; -@@ -145,7 +145,7 @@ - - my $hts_lib = "$root/lib"; - my $hts_include = "$root/include/htslib"; -- if (-f "$hts_lib/libhts.a" && -f "$hts_include/hts.h") { -+ if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") { - $self->config_data('hts_lib' => $hts_lib); - $self->config_data('hts_include' => $hts_include); - return 1; -@@ -164,7 +164,7 @@ - This module requires htslib (http://htslib/org) - Install it if you have not done so already. - --This script will attempt to locate htslib by looking for hts.h and libhts.a in: -+This script will attempt to locate htslib by looking for hts.h and libhts.so/libhts.a in: - - 1. --htslib command line argument - 2. HTSLIB_DIR environment variable diff --git a/dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch b/dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch deleted file mode 100644 index d68bc54e40d..00000000000 --- a/dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch +++ /dev/null @@ -1,48 +0,0 @@ ---- a/Build.PL -+++ b/Build.PL -@@ -68,7 +68,13 @@ - # If either of these are set, we expect to find the htslib files there: - # (They're explicitly set by the user, so we shouldn't fall back to - # finding another copy somewhere else.) -- if (my $dir = $self->args('htslib')) { -+ if (my ($incdir, $libdir) = ($self->args('htslib-includedir'), $self->args('htslib-libdir'))) { -+ return 1 if $self->find_hts_in_split_install_dirs($incdir, $libdir); -+ $self->die_hts_not_found( -+ "--htslib-includedir '$incdir' or --htslib-libdir '$libdir' command line parameters do not contain expected files\n" -+ ); -+ } -+ elsif (my $dir = $self->args('htslib')) { - return 1 if $self->find_hts_in_build_dir($dir); - return 1 if $self->find_hts_in_install_dir($dir); - $self->die_hts_not_found( -@@ -155,6 +161,22 @@ - } - } - -+sub find_hts_in_split_install_dirs { -+ my ($self, $hts_include, $hts_lib) = @_; -+ -+ chomp($hts_include); -+ chomp($hts_lib); -+ -+ if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") { -+ $self->config_data('hts_lib' => $hts_lib); -+ $self->config_data('hts_include' => $hts_include); -+ return 1; -+ } -+ else { -+ return 0; -+ } -+} -+ - sub die_hts_not_found { - my ($self, $msg) = @_; - -@@ -166,6 +188,7 @@ - - This script will attempt to locate htslib by looking for hts.h and libhts.so/libhts.a in: - -+ 0. --htslib-includedir and --htslib-libdir command line arguments - 1. --htslib command line argument - 2. HTSLIB_DIR environment variable - 3. --prefix command line argument (which also sets installation location)