gentoo resync : 14.07.2018

4 files changed, 0 insertions, 117 deletions

diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild
deleted file mode 100644
index e5c23d67da05..000000000000
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild
+++ /dev/null
@@ -1,31 +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=2.11
-
-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}/2.11-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
deleted file mode 100644
index c82f5a3486d0..000000000000
--- a/dev-perl/Bio-DB-HTS/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX 2.11-build_split_htslib_opts.patch 2453 BLAKE2B 19f99d0a56db7c4778bc478cd952062e8095997fe9028b6c7e251e2391f9f074774bdaec6db7c610488a921a73abf83edeee2b5f5a5185d4bb422c5dff6a8634 SHA512 4770ebb1bf8fdc3e51f4a020db1c45befa64478bd2cf2d77397e5e7ac09d34d17457ecd2be2fd53062ada48f579621cb959c245493906b9c04367142b27a2fa8
-DIST Bio-DB-HTS-2.11.tar.gz 5250814 BLAKE2B d77ccacebf339a33ab106b997139cdbf79f6c28269a832305e660b28370aca82b4c9824773acdbf8f59b18dd61f40346a9870578dba7b5b989b0f3bc9ad14b35 SHA512 114d90fe92b684250183b45b4d23d2dd45ecdcb2fa54f7b1c311ed668d8e87953adb861f709a0a48ff2b873ce777b21bc3b557bafa0df216b9a71b59facff6fd
-EBUILD Bio-DB-HTS-2.11.ebuild 639 BLAKE2B 9761dddc9216bc11e3a167d067b6d33fc4a8f7b7aeaf690a02c3816620bc10fd9a6d306def470dd056de0958538433a784a62328f48aa4447b7c437460881c44 SHA512 789ad5439ac7014585b61ac11790fff6c6786fb5c249a7e895fcc6c7a988e4f61e097d98883cb36203e0ab030fc874f38dfbd969e0a3b6c9c6a61a33b90f3e9e
-MISC metadata.xml 555 BLAKE2B fe8d2547a6d959f24231c15b5803e8e71dd94ac0d865dd0a53dff97c62b39db8ff40f845f7d4a48cd4dc19d31c044e06ca8394d745a79c532fc61e96a66dab3f SHA512 9e03a79d88ca855783562bd5d3b9a4f71698c2caae43c009bbcf312bd5810d362842cb4e834291b08a5231785f59fc5598edca6868716d5a7487716d10acac39
diff --git a/dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch b/dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch
deleted file mode 100644
index 727c500360d1..000000000000
--- a/dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch
+++ /dev/null
@@ -1,65 +0,0 @@
-diff --git a/Build.PL b/Build.PL
-index 0d684b7..87a223b 100644
---- a/Build.PL
-+++ b/Build.PL
-@@ -68,7 +68,15 @@ sub find_hts {
-     # 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')) {
-+    my $incdir = $self->args('htslib-includedir');
-+    my $libdir = $self->args('htslib-libdir');
-+    if ($incdir && $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);
-         $self->die_hts_not_found(
-@@ -158,6 +166,23 @@ sub find_hts_in_install_dir {
-     }
- }
- 
-+sub find_hts_in_split_install_dirs {
-+    my ($self, $hts_include, $hts_lib) = @_;
-+
-+    chomp($hts_lib);
-+    chomp($hts_include);
-+    $hts_include =~ s{include/htslib$}{include};
-+
-+    if (hts_dev_files_exist($hts_lib, $hts_include)) {
-+        $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) = @_;
- 
-@@ -170,12 +195,13 @@ Install it if you have not done so already.
- This script will attempt to locate HTSlib by looking for htslib/hts.h
- and libhts.a / libhts.so in:
- 
--  1. --htslib command line argument
--  2. HTSLIB_DIR environment variable
--  3. --prefix command line argument (which also sets installation location)
--  4. Alien::HTSlib dependency resolver
--  5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
--  6. common library locations: /usr /usr/local, /usr/share, /opt/local
-+  1. --htslib-includedir and --htslib-libdir command line arguments
-+  2. --htslib command line argument
-+  3. HTSLIB_DIR environment variable
-+  4. --prefix command line argument (which also sets installation location)
-+  5. Alien::HTSlib dependency resolver
-+  6. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
-+  7. common library locations: /usr /usr/local, /usr/share, /opt/local
- 
- END
- 
diff --git a/dev-perl/Bio-DB-HTS/metadata.xml b/dev-perl/Bio-DB-HTS/metadata.xml
deleted file mode 100644
index 95abbb699ad4..000000000000
--- a/dev-perl/Bio-DB-HTS/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>marecki@gentoo.org</email>
-		<name>Marek Szuba</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">Ensembl/Bio-DB-HTS</remote-id>
-		<remote-id type="cpan">Bio-DB-HTS</remote-id>
-		<remote-id type="cpan-module">Bio::DB::HTS</remote-id>
-	</upstream>
-</pkgmetadata>