sci-biology/profphd: Fix for newer perl, version Bump

Package-Manager: portage-2.2.10/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 88 insertions, 10 deletions

diff --git a/sci-biology/profphd/ChangeLog b/sci-biology/profphd/ChangeLog
index 5f1300e41b35..5b29b3af77b8 100644
--- a/sci-biology/profphd/ChangeLog
+++ b/sci-biology/profphd/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/profphd
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/ChangeLog,v 1.3 2013/04/24 14:28:05 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/ChangeLog,v 1.4 2014/04/24 11:38:57 jlec Exp $
+
+*profphd-1.0.40 (24 Apr 2014)
+
+  24 Apr 2014; Justin Lecher <jlec@gentoo.org> profphd-1.0.39.ebuild,
+  +profphd-1.0.40.ebuild, +files/profphd-1.0.39-perl.patch:
+  Fix for newer perl, version Bump
 
   24 Apr 2013; Justin Lecher <jlec@gentoo.org> profphd-1.0.39.ebuild:
   Updated deps
diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest
index 7038e8ce318a..691620115325 100644
--- a/sci-biology/profphd/Manifest
+++ b/sci-biology/profphd/Manifest
@@ -1,14 +1,29 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA512
 
+AUX profphd-1.0.39-perl.patch 376 SHA256 3452144a6f1dade6ab5219b757975002b617b04b1da151593e810bbd561be500 SHA512 e4004dbb835560b3a2aa140aea0ed57812ee9dc11dc18fb7b1dbdeee73bacfef3fecfd686f15fa87cde5597ddb322057d67fa61708ba3077c5449f93a0284b8e WHIRLPOOL 5fd5111f9f5075a7533b5af6e72976cab6404f36b3be3558809815553243aaad4e763e7cc1ec8e06c3c841617200c9c7396aa64c4728f6224b4879416de8f3b8
 DIST profphd-1.0.39.tar.xz 4406776 SHA256 4ff67e7b4dcb5748ee5115f1e7b9de7de6ca1c5a7982971a7147fe4ee5a5d288 SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b WHIRLPOOL 7e149f3e724ae5e727810ace6a1063708c35bb957861e4873c0763e48af5362ea50757d94c592052fec9d6e63767d036a39104a72ba6deb981c1f6023f19464e
-EBUILD profphd-1.0.39.ebuild 893 SHA256 f7ada60c521ad981e95e825e21b9ad423360e6f9d61e0bc3fa08113c72dd4841 SHA512 2fe94fb6dd0c02b97e2ec163ca82361428002e8354aece00ad3b007c418066663c7241bb495cf6d04268b8433f15911bfc8360a2bceb32189fe9af24b6ff043b WHIRLPOOL 9ffe526ed89da3fc91f6685a2ddad6002eb07252e0cd360dfc04ef649b095e8cff1245921522643ed4e43a3b36c5164018ab16a785bdb3dc982950a770bef5de
-MISC ChangeLog 529 SHA256 50d38d679c6fc09a8efec9d5754964258490168bcebb5317ae7289e67f0f758a SHA512 23d8321f958ca257ce2aed6c61046fc35a916aec3549efba936f16ae9040e40edf657c542eebf8c292a1dbe01ffab035a10de8f51b0e3fc017dfada9933a0b4d WHIRLPOOL dd5edf41c4a6cba583318d289bc95c91c4d83cc0cd58eabe2ac738d1b8f856c0f2d6e1d86514af9fd246a11866fd0b6cf22db5c218d25fd453962a7e9fa347e5
+DIST profphd-1.0.40.tar.xz 4491592 SHA256 50c85da552993758df191e3e06910fb221a156a8eaba94badf5a716b04648c5c SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3 WHIRLPOOL 4d7ac3cf32607cefc983116fa8fe8e795e92e89590bd612a2180e9fd59ec5c60220b065a2fddf3552aa81a3d02f852a36e08086d0867ac28ded2faf0d31a38ad
+EBUILD profphd-1.0.39.ebuild 947 SHA256 7bb9ab3b9a03092a8fb82beccd09f8180137de6303c23eab4ff70c52c13f2791 SHA512 395d206b8ef1052a479f3d48fe2a3f36edab70643dc440b8b34a305d8b039b0b906c44d745050403a46ce2e07bb03f82da46f50a0e55efc430f7225915e83137 WHIRLPOOL d00f4c5003b7270188fd9f775f702f7e3748ac89c8b23a993764eee28eae95a9070a74dd8c6498976e40920caba6d5ab460cbb4485dc73fc1228765ae188d3b4
+EBUILD profphd-1.0.40.ebuild 955 SHA256 b68d64404c70758d249ca9842e49a037f8390e025648fbf46b52c91905754b87 SHA512 cf99a163815f28ff5b6058b9db26ee311071fc3545c8aed8e4a53de2ae39716dc920c0fe7a818d8ffae90c9275a18214c4798cd1e605bc0f3d65ba99538d7ec5 WHIRLPOOL 78bf16fff3d8b7e4bbcb780d0e5b446ee5b13427a3322c2c26143deff5cc4ae1a0a9afcf42c778250cb97773d317066044efdcf4fe0f402e1c78f5c5318ce245
+MISC ChangeLog 726 SHA256 6b1b7fe7d0c46bcdc7cec211cbaccc8760e115256be3533b14356084cf707b7b SHA512 fa760ad44e8fdfe6c16727e6b2c8820ccbb1d06df9f1a1d6750876ed734fadcbc39fb56d5e3c7098b479500b880e236a8f744c17b257b997a3a06e0fe0ef81e6 WHIRLPOOL 3eb1e886b3d977cbc425e4be86c25d2f1804cfadd66c6ad09bdf6dd023bd0e7afba1807b08d3ee9de64888f6e91c86b48ada852054f6a0a40283fadbd434679a
 MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/profphd/files/profphd-1.0.39-perl.patch b/sci-biology/profphd/files/profphd-1.0.39-perl.patch
new file mode 100644
index 000000000000..10682271601c
--- /dev/null
+++ b/sci-biology/profphd/files/profphd-1.0.39-perl.patch
@@ -0,0 +1,16 @@
+ src/prof/prof | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/prof/prof b/src/prof/prof
+index 4f26024..356442d 100755
+--- a/src/prof/prof
++++ b/src/prof/prof
+@@ -238,7 +238,7 @@ See each keyword for more help.  Most of these are likely to be broken.
+ 
+ alternative connectivity patterns (default=3)
+ 
+-=item 3
++=item C<3>
+ 
+ predict sec + acc + htm
+ 
diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild
index 77e853cd685c..72bf2e8fff12 100644
--- a/sci-biology/profphd/profphd-1.0.39.ebuild
+++ b/sci-biology/profphd/profphd-1.0.39.ebuild
@@ -1,9 +1,11 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/profphd-1.0.39.ebuild,v 1.3 2013/04/24 14:28:05 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/profphd-1.0.39.ebuild,v 1.4 2014/04/24 11:38:57 jlec Exp $
 
 EAPI=5
 
+inherit eutils
+
 DESCRIPTION="Secondary structure and solvent accessibility predictor"
 HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
 SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
@@ -24,6 +26,7 @@ src_prepare() {
 	sed \
 		-e '/ln -s/s:prof$:profphd:g' \
 		-i src/prof/Makefile || die
+	epatch "${FILESDIR}"/${P}-perl.patch
 }
 
 src_compile() {
diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild
new file mode 100644
index 000000000000..0995a72af1a7
--- /dev/null
+++ b/sci-biology/profphd/profphd-1.0.40.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/profphd/profphd-1.0.40.ebuild,v 1.1 2014/04/24 11:38:57 jlec Exp $
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Secondary structure and solvent accessibility predictor"
+HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
+SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}
+	dev-perl/librg-utils-perl
+	sci-libs/profnet
+	sci-libs/profphd-utils
+"
+
+src_prepare() {
+	sed \
+		-e '/ln -s/s:prof$:profphd:g' \
+		-i src/prof/Makefile || die
+	epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch
+}
+
+src_compile() {
+	emake prefix="${EPREFIX}/usr"
+}
+
+src_install() {
+	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
+}