gentoo Easter resync : 12.04.2020

4 files changed, 30 insertions, 5 deletions

diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.110.0.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.110.0.ebuild
index 745f39851f38..76af57429d3d 100644
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.110.0.ebuild
+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.110.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -24,6 +24,7 @@ DEPEND="${RDEPEND}
 	test? ( dev-perl/Test-LeakTrace )"
 
 PATCHES=(
+	"${FILESDIR}/2.11-build_env_ldflags.patch"
 	"${FILESDIR}/2.11-build_split_htslib_opts.patch"
 )
 
diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0.ebuild
index a09e9096e925..575961ddaf10 100644
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0.ebuild
+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-3.10.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -12,7 +12,7 @@ DESCRIPTION="Perl bindings for sci-libs/htslib"
 
 LICENSE="Apache-2.0"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 x86"
 IUSE="test"
 
 RESTRICT="!test? ( test )"
@@ -24,6 +24,7 @@ DEPEND="${RDEPEND}
 	test? ( dev-perl/Test-LeakTrace )"
 
 PATCHES=(
+	"${FILESDIR}/2.11-build_env_ldflags.patch"
 	"${FILESDIR}/2.11-build_split_htslib_opts.patch"
 )
 
diff --git a/dev-perl/Bio-DB-HTS/Manifest b/dev-perl/Bio-DB-HTS/Manifest
index feb6876d9ecf..b07629e9be8a 100644
--- a/dev-perl/Bio-DB-HTS/Manifest
+++ b/dev-perl/Bio-DB-HTS/Manifest
@@ -1,6 +1,7 @@
+AUX 2.11-build_env_ldflags.patch 819 BLAKE2B 7c082fbe66b3b75a81e7fc660ff202a34fa26a0fa07e350b16d0f06befdff8535c728aafdb735a19344615b27efc6fca72ca9e5a90b03c7ed4e85fcd56e31a33 SHA512 22cb4edc3a2ad20130f24675e814c6167a63ab89c2b1c3551eed0099937a0692cebd5ceefa6616302defaae25712651fb3ed8863031b75c15822173390b4d52c
 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
 DIST Bio-DB-HTS-3.01.tar.gz 5250834 BLAKE2B ca7d3dfb6886460e7beee495eaa6857c912dc6bff24c1c8b888e7ada5ca736035af7ee48adeb5dd3b10204f99be4d0e2cb8d6350fa3e7bfe3fb1299e935ddc4e SHA512 4a464ffb300edf8ed8839c4d788a7c53d2a2cdc5abd675b8648d42e0b60f78b905dfb81cf1396daddbf2e279db2819df250117ecebdc3de5fdcb94a812182255
-EBUILD Bio-DB-HTS-2.110.0.ebuild 664 BLAKE2B 2de5ed54fb566778c8890abbed2add01c1b21ac05d872e97e0c82edf435bf00dd9d993772d3b73f04829660de09d3614dab736e8a8ffbaec409e2ca831a7ff3a SHA512 227ca027ccd6a1be3fafddbed445f05d220b228f194a03f19b6fc211f8d222f6dc25d36799d607e08d75d435494c3fe2017eb1f585c8fd9415dd8835e31c57bb
-EBUILD Bio-DB-HTS-3.10.0.ebuild 664 BLAKE2B fe5a176b0e4117f5b88dd31e4f53a6ac30b3c6ebc5dadf73ba82aa5029180ea9032062e891a499458ad8cf6599a0a3d18fcbaf7fa24483e446551b9d6ab8744d SHA512 c8cad91349f4878a1848529b982d142b92640da4ff49e5b28cada9015679a62cea66e658761b1f8339b6b597b5be267962651466380e0123109b9bd1f418b4db
+EBUILD Bio-DB-HTS-2.110.0.ebuild 708 BLAKE2B 0e10e42a145505e7445687411f809c8810f3b052e2695ed93b44aa4ae603692a4431038ed385bcd4bd90b85f8c9bd6938643ebd79a4cbc20eaf2f50877849ff2 SHA512 a9930cf078bb84e03b5281774ef3b98c712cb1c8d62e865487978af568659fcaa445263c40fba2bc01cf7a3ee25e5e2f302238e29acee6826b6f1ae4a4d467ea
+EBUILD Bio-DB-HTS-3.10.0.ebuild 706 BLAKE2B dd60fd553fc822310aa4a75f43fd76748544c58edd6e1d89ea8f8426e5625738db71978d6a7d84f269f2a5dda2ee8c83487f61b5e56f0721f1886313b4fef953 SHA512 daf5fa2771c1d85f52ac9d6ec5b4453360701793ae479876cbe4792e6ef84f3f7290229e4d83cd62cfb24b1af81f11d461fc1f4d3828b8e1a9ab9710638b86b9
 MISC metadata.xml 555 BLAKE2B fe8d2547a6d959f24231c15b5803e8e71dd94ac0d865dd0a53dff97c62b39db8ff40f845f7d4a48cd4dc19d31c044e06ca8394d745a79c532fc61e96a66dab3f SHA512 9e03a79d88ca855783562bd5d3b9a4f71698c2caae43c009bbcf312bd5810d362842cb4e834291b08a5231785f59fc5598edca6868716d5a7487716d10acac39
diff --git a/dev-perl/Bio-DB-HTS/files/2.11-build_env_ldflags.patch b/dev-perl/Bio-DB-HTS/files/2.11-build_env_ldflags.patch
new file mode 100644
index 000000000000..eef077914183
--- /dev/null
+++ b/dev-perl/Bio-DB-HTS/files/2.11-build_env_ldflags.patch
@@ -0,0 +1,22 @@
+--- a/Build.PL
++++ b/Build.PL
+@@ -107,11 +107,17 @@
+     my $hts_include = $self->config_data('hts_include');
+     my $hts_lib     = $self->config_data('hts_lib');
+     my $static      = $self->args('static');
++
++    my @env_linker_flags;
++    if ( defined $ENV{LDFLAGS} ) {
++        @env_linker_flags = split qr{\s+}, $ENV{LDFLAGS};
++    }
++
+     $self->include_dirs([$hts_include]);
+     if($static){
+-      $self->extra_linker_flags("-L$hts_lib", '-lhts', '-lpthread', '-lz');
++      $self->extra_linker_flags(@env_linker_flags, "-L$hts_lib", '-lhts', '-lpthread', '-lz');
+     }else{
+-      $self->extra_linker_flags("-L$hts_lib", "-Wl,-rpath,$hts_lib", '-lhts', '-lpthread', '-lz');
++      $self->extra_linker_flags(@env_linker_flags, "-L$hts_lib", "-Wl,-rpath,$hts_lib", '-lhts', '-lpthread', '-lz');
+     }
+ }
+