From 3cf7c3ef441822c889356fd1812ebf2944a59851 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Tue, 25 Aug 2020 10:45:55 +0100
Subject: gentoo resync : 25.08.2020

---
 sci-libs/htslib/Manifest             |  4 +--
 sci-libs/htslib/htslib-1.10.2.ebuild | 51 ++++++++++++++++++++++++++++++++++++
 sci-libs/htslib/htslib-1.5.ebuild    | 37 --------------------------
 3 files changed, 53 insertions(+), 39 deletions(-)
 create mode 100644 sci-libs/htslib/htslib-1.10.2.ebuild
 delete mode 100644 sci-libs/htslib/htslib-1.5.ebuild

(limited to 'sci-libs/htslib')

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 367d9aa3cd48..3f1f8ecec673 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,5 +1,5 @@
-DIST htslib-1.5.tar.bz2 1051132 BLAKE2B 90c6aeeaa2a2692228aa1f530d775a6e81f9275d321e8b2d6005b86b9a25e5967acca19dd898311a5bc4f3c17d4e8ea36d18da4602e18fadee47666350122077 SHA512 fd58552ddbd178f9797123fdaf47914ccd0e2aefd055fc6557ac8f479c600775616107cfa871c3acd93079f45974a19f443941a79f2acfd2a8c2983ef35b8917
+DIST htslib-1.10.2.tar.bz2 1306320 BLAKE2B f877bd9c160921f498f4160f687094a1a369732bc9f61cd94a3c9ca311fa9f865505a205e38e0d348a1010b627f1ef07b590cd7e69c945df1d804133b17b2fd1 SHA512 3ecb83b0abccf731cd42b889e352e10dd922524f6e78bcafb04f8c6c71457b0dc1f5f22690b36f03cce7d97a6a905db286243ef4858138068dcac368e4ae1075
 DIST htslib-1.9.tar.bz2 1178859 BLAKE2B a0229313d3572717101f4f23d39fa124f3bb38d8b2e65055f4f801dbb5f1549df95115e8beadd8fa024171b3ff8a874d20087bf71819c36700666f168dbe41ab SHA512 ddb0e2d970e4c2c27e203b064898f95cb7c187cd497c02fc7b4312dcea25669d0b6063d537687521e7a065f6daefa1ae897add2df4981037a187b499d08fdef7
-EBUILD htslib-1.5.ebuild 769 BLAKE2B 0a40bc1059beabd9671df35ea8febf7b5a11c8b46aa0f66891879962698789b36326fd91423200312497b2f9691766c1dc8aae5dceab5626a7e8de119881793a SHA512 e5df03c2dfa5088743674af125f7464a6e2add8d9c092060d7ddfc914cac4cff16d65eabb35ca3c199290461b92f7424a4347fded4f76dce763801b2b70f91c2
+EBUILD htslib-1.10.2.ebuild 1041 BLAKE2B 12d35fa9397f441d9e1ee444abca8c56cf87bf16aa2b82b0d6d0bad6ec27546dccdb4b540eaca322f5208eb7c0a6b9f6de5cfa8762641d73a3f40fd8bee5ea47 SHA512 99c54c20f1f01fc243bc7cb25325265e1d959fdc23a3d2db4c2cef29fb9f74cc423835a25d9f5fa1b5af027413caeb6ee8fff2f517ae2dbe8119b80c504b87d9
 EBUILD htslib-1.9.ebuild 943 BLAKE2B 7aafc2a82f264c4bffc1fc527f41ee336bba5b92b02c0a7e5dd3ed752b24fe3f398a375b159a1f6d9630af05b73815cb7bf748a6637cceac13cc13006daaceec SHA512 f865568b71ccda72f1c40622dc51f5e7bba5c9f958d1c7f5637373241655c9d013d2e454f39ca4a803f1ed6d6303b4b6f33df388046b400a1a656d50d8fa9ced
 MISC metadata.xml 349 BLAKE2B 0a67c5034cea0b990b01f90cf319622a73d2c8c23b89d207f013f1ac27fbfd2f267f4d0a8d331b9ab9de792cea9914671cfb2568a56fc09aeec890f69934e943 SHA512 9108691a0c4c68ececa5e93d1719b4a6fc42c423c0b7dca3c037007873a40c86a44610c54139c6868391bb903d509b0202a87640d7114815d07ef62e478ffce7
diff --git a/sci-libs/htslib/htslib-1.10.2.ebuild b/sci-libs/htslib/htslib-1.10.2.ebuild
new file mode 100644
index 000000000000..67a341be70e3
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.10.2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+	bzip2? ( app-arch/bzip2:= )
+	curl? ( net-misc/curl )
+	lzma? ( app-arch/xz-utils:= )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	default
+
+	# upstream injects LDFLAGS into the .pc file,
+	# which is a big nono for QA
+	sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+		-i htslib.pc.in || die
+}
+
+src_configure() {
+	econf \
+		--disable-gcs \
+		--disable-plugins \
+		--disable-s3 \
+		$(use_enable bzip2 bz2) \
+		$(use_enable curl libcurl) \
+		$(use_enable lzma)
+}
+
+src_compile() {
+	emake AR="$(tc-getAR)"
+}
+
+src_install() {
+	default
+
+	# doesn't use libtool, can't disable static libraries
+	find "${ED}" -name '*.a' -delete || die
+}
diff --git a/sci-libs/htslib/htslib-1.5.ebuild b/sci-libs/htslib/htslib-1.5.ebuild
deleted file mode 100644
index d9957ce3a171..000000000000
--- a/sci-libs/htslib/htslib-1.5.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="C library for high-throughput sequencing data formats"
-HOMEPAGE="http://www.htslib.org/"
-SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
-
-SLOT="0/2"
-LICENSE="MIT"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +lzma static-libs"
-
-RDEPEND="
-	bzip2? ( app-arch/bzip2 )
-	curl? ( net-misc/curl )
-	lzma? ( app-arch/xz-utils )"
-DEPEND="${RDEPEND}"
-
-src_configure() {
-	econf \
-		--disable-gcs \
-		--disable-plugins \
-		--disable-s3 \
-		$(use_enable bzip2 bz2) \
-		$(use_enable curl libcurl) \
-		$(use_enable lzma)
-}
-
-src_install() {
-	default
-
-	if ! use static-libs; then
-		find "${D}" -name '*.a' -delete || die
-	fi
-}
-- 
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