gentoo resync : 02.05.2018

4 files changed, 73 insertions, 36 deletions

diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild
index 02c38cd34f33..e5c23d67da05 100644
--- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild
+++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.11.ebuild
@@ -4,7 +4,7 @@
 EAPI=6
 
 DIST_AUTHOR=AVULLO
-DIST_VERSION=2.10
+DIST_VERSION=2.11
 
 inherit perl-module
 
@@ -15,16 +15,17 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="test"
 
-RDEPEND="sci-libs/htslib:="
+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}/2.11-build_split_htslib_opts.patch"
 )
 
 src_configure() {
-	local myconf="--htslib=${EPREFIX}/usr"
+	local myconf="--htslib-includedir=${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 850f18da3d89..c82f5a3486d0 100644
--- a/dev-perl/Bio-DB-HTS/Manifest
+++ b/dev-perl/Bio-DB-HTS/Manifest
@@ -1,4 +1,4 @@
-AUX 2.10-build_search_for_so.patch 1169 BLAKE2B 53e0eaf90d50cc3571a55083db1e48a908c9d05fda46d3e3fb1c61f0c426ea1dc8a263512adcf7ab58eed8b7f217e50db961e96483b3599afc4077c22e64d81c SHA512 39ee373385be49f143c20d0cb6794debd008affe1101f991cc924a163853e2884508753c811f506bcd97d7545599edb735efff64dfc36269d0964c15a70389b7
-DIST Bio-DB-HTS-2.10.tar.gz 5245650 BLAKE2B a52d9b1e19d5920d61dd365eacfd1a40726500e25a3ab516df5a1d59a7a9d79ce02db7a2145801b6af5df2c41c95e80b49a39db83d27fd7ff3cf88ba0e6a328d SHA512 4e7c01022d9edf48a0e0dcffcbccf34812f236d1b581760ac115c323de5779fb6212eb4ad7d1953811930a6137cc8f5f59028c73d645d1ca5fb6118dd846ad57
-EBUILD Bio-DB-HTS-2.10.ebuild 543 BLAKE2B 95d0cdb4cff8ead7a2427ea3663d61ba7a18582eb925effc84e0072f5a35b87d5082e30a386fa0d1c3d5a8bb2ef4584296ffa19b867c59c8b5f8f0da92666727 SHA512 5c22659c738f9e529a77723eb8f458c5a0bb1ca45be3ba107acee973faec10af1e32a0aa1a1402cf589d7cd8acc827e414429f3ba6315801d814f3c881139a3b
+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/2.10-build_search_for_so.patch b/dev-perl/Bio-DB-HTS/files/2.10-build_search_for_so.patch
deleted file mode 100644
index b3d11bbbe7aa..000000000000
--- 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/2.11-build_split_htslib_opts.patch b/dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch
new file mode 100644
index 000000000000..727c500360d1
--- /dev/null
+++ b/dev-perl/Bio-DB-HTS/files/2.11-build_split_htslib_opts.patch
@@ -0,0 +1,65 @@
+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
+