Added missing header files for BioPerl, backported fix to 1.8 branch (fixes bug #145562, see also bug #120446)

(Portage version: 2.1.1)
 (Unsigned Manifest commit)

3 files changed, 22 insertions, 52 deletions

diff --git a/sci-libs/io_lib/Manifest b/sci-libs/io_lib/Manifest
index c58a6cde3fa3..e82d1d53bcdb 100644
--- a/sci-libs/io_lib/Manifest
+++ b/sci-libs/io_lib/Manifest
@@ -1,24 +1,31 @@
-DIST io_lib-1.8.12b.tar.bz2 259252
+DIST io_lib-1.8.12b.tar.bz2 259252 RMD160 45327d7094a24c3f1c1144f662239928b4ff0d22 SHA1 16d24646fcf96e0766f2a0878338fead17d607ce SHA256 230e4b58d30201057b7f0baf386d77addee6352e3481be2ecbe5415146ce05bc
 DIST io_lib-1.9.0.tar.bz2 256883 RMD160 c90abf6466ce1bf8b9bd59ce1401c88a83b2aaad SHA1 401fc909021019367acaf2e846b44cdc006dab64 SHA256 99848f286967e9e1cb123c2b607332edb766f7290c5b93fb87fe58a39b9dddaa
+EBUILD io_lib-1.8.12b-r1.ebuild 714 RMD160 bb1dc423266ecda65146fa860bb786a5cab5a1d6 SHA1 e147bd1eaddeda963b2815a888a3601b3fa302d1 SHA256 7af7f2520ca8676a29425ec1e04fff58643b3e87b1aa8dbe92a83b7f34e85450
+MD5 c21500b4e97c8f9ebdfe80fc37f2d20f io_lib-1.8.12b-r1.ebuild 714
+RMD160 bb1dc423266ecda65146fa860bb786a5cab5a1d6 io_lib-1.8.12b-r1.ebuild 714
+SHA256 7af7f2520ca8676a29425ec1e04fff58643b3e87b1aa8dbe92a83b7f34e85450 io_lib-1.8.12b-r1.ebuild 714
 EBUILD io_lib-1.8.12b.ebuild 565 RMD160 c5d431fb5024759b6959de7001d3878a419726ab SHA1 96e21e955840428bcbc2341ce9befba264aa8b4e SHA256 2cb376d2b2b80125bbd22eb624a71776f724dad7125c85cd2d35a5f95972c7f1
 MD5 def1150c584b7f69a73f92e9e9d46eb5 io_lib-1.8.12b.ebuild 565
 RMD160 c5d431fb5024759b6959de7001d3878a419726ab io_lib-1.8.12b.ebuild 565
 SHA256 2cb376d2b2b80125bbd22eb624a71776f724dad7125c85cd2d35a5f95972c7f1 io_lib-1.8.12b.ebuild 565
-EBUILD io_lib-1.9.0.ebuild 823 RMD160 ecd8c6ed64e165c3c3073f20d2fce1f919086494 SHA1 1d9d4af2793070945bbec97b65b705a77c1795b4 SHA256 a3008ecbb3131c6d5d1e2dadb9353ee5c842efcd7dd570ba80f4e8e5851aa686
-MD5 3b3d8bf5ede60e965ac2f7a263768371 io_lib-1.9.0.ebuild 823
-RMD160 ecd8c6ed64e165c3c3073f20d2fce1f919086494 io_lib-1.9.0.ebuild 823
-SHA256 a3008ecbb3131c6d5d1e2dadb9353ee5c842efcd7dd570ba80f4e8e5851aa686 io_lib-1.9.0.ebuild 823
-MISC ChangeLog 1031 RMD160 6fdce9082cb0459f9a51443c1ac6b111e00adfaf SHA1 bc723b51baed9f8411a40d17d24e42d01aa627eb SHA256 9c12109d2df683e42cc8f1be89d6a48fec886fcc58bdbaab6265fb1cd11bba39
-MD5 f8c50861cd8352ca1bff54ed787edbf5 ChangeLog 1031
-RMD160 6fdce9082cb0459f9a51443c1ac6b111e00adfaf ChangeLog 1031
-SHA256 9c12109d2df683e42cc8f1be89d6a48fec886fcc58bdbaab6265fb1cd11bba39 ChangeLog 1031
+EBUILD io_lib-1.9.0-r1.ebuild 886 RMD160 e3f0daede3a0de5d9cbd36e26886c42f97d1c93f SHA1 90be974850f10257fea5a36d79cc716b8bba6b05 SHA256 dfa9a43f9fa9ed19ddcf06675c879be2a14f91712ff43da628231b001296a6b7
+MD5 eadd0c2f7a7f81eb9d609823d9a0e961 io_lib-1.9.0-r1.ebuild 886
+RMD160 e3f0daede3a0de5d9cbd36e26886c42f97d1c93f io_lib-1.9.0-r1.ebuild 886
+SHA256 dfa9a43f9fa9ed19ddcf06675c879be2a14f91712ff43da628231b001296a6b7 io_lib-1.9.0-r1.ebuild 886
+MISC ChangeLog 1532 RMD160 5e0f76695ee16df0d128e4c1ec13fccc85552a9c SHA1 200ffc39342d4c058ed1da1375258381405ae10c SHA256 101e09314daf6fa8c14854f744279ee4f93ca8a0579f822906d7bbf6ee865133
+MD5 09cee5e5a5e1b017d063ca79b1e91c7e ChangeLog 1532
+RMD160 5e0f76695ee16df0d128e4c1ec13fccc85552a9c ChangeLog 1532
+SHA256 101e09314daf6fa8c14854f744279ee4f93ca8a0579f822906d7bbf6ee865133 ChangeLog 1532
 MISC metadata.xml 254 RMD160 f02847af149737bf8044b3de239c5bd4b42abca5 SHA1 39b2c27b727742ea30045ab645b5a3ef433247a6 SHA256 3392ded43ad861595a8cfeb0441342fdbcd6e731b4793c3e8a22ff927ce09f27
 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
 RMD160 f02847af149737bf8044b3de239c5bd4b42abca5 metadata.xml 254
 SHA256 3392ded43ad861595a8cfeb0441342fdbcd6e731b4793c3e8a22ff927ce09f27 metadata.xml 254
-MD5 1670ca8a79d13eea06cd7f4945e0f392 files/digest-io_lib-1.8.12b 67
-RMD160 26ac785c42cf2566cabe8f21e0ea4f058995c0c1 files/digest-io_lib-1.8.12b 67
-SHA256 ea733807c82af459b273d3a914a1a07acec85abbbf4677dd473ee1e63eceef4c files/digest-io_lib-1.8.12b 67
-MD5 96a76b8141204f2eae5049c52efbeecf files/digest-io_lib-1.9.0 241
-RMD160 969fc2d15bac1dd87558a0f959a2143f3661c289 files/digest-io_lib-1.9.0 241
-SHA256 d9e52fdaa7db569d098c0affd098edc7cb3ac867792a108a7196e0f742a3ab20 files/digest-io_lib-1.9.0 241
+MD5 be6345fd42e8994cb6485c786a5f9f09 files/digest-io_lib-1.8.12b 247
+RMD160 eabd20852a8aa54c15a0c20f72db3a8981a8756e files/digest-io_lib-1.8.12b 247
+SHA256 1205d6ca830fd3a9c83b891fb812d41ecdb5779f9e91e98a81f3e61bf5957a33 files/digest-io_lib-1.8.12b 247
+MD5 be6345fd42e8994cb6485c786a5f9f09 files/digest-io_lib-1.8.12b-r1 247
+RMD160 eabd20852a8aa54c15a0c20f72db3a8981a8756e files/digest-io_lib-1.8.12b-r1 247
+SHA256 1205d6ca830fd3a9c83b891fb812d41ecdb5779f9e91e98a81f3e61bf5957a33 files/digest-io_lib-1.8.12b-r1 247
+MD5 96a76b8141204f2eae5049c52efbeecf files/digest-io_lib-1.9.0-r1 241
+RMD160 969fc2d15bac1dd87558a0f959a2143f3661c289 files/digest-io_lib-1.9.0-r1 241
+SHA256 d9e52fdaa7db569d098c0affd098edc7cb3ac867792a108a7196e0f742a3ab20 files/digest-io_lib-1.9.0-r1 241
diff --git a/sci-libs/io_lib/files/digest-io_lib-1.9.0 b/sci-libs/io_lib/files/digest-io_lib-1.9.0
deleted file mode 100644
index 0bdd84e12a91..000000000000
--- a/sci-libs/io_lib/files/digest-io_lib-1.9.0
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 9324dc5a3f44895175b3bc2f0bc045d0 io_lib-1.9.0.tar.bz2 256883
-RMD160 c90abf6466ce1bf8b9bd59ce1401c88a83b2aaad io_lib-1.9.0.tar.bz2 256883
-SHA256 99848f286967e9e1cb123c2b607332edb766f7290c5b93fb87fe58a39b9dddaa io_lib-1.9.0.tar.bz2 256883
diff --git a/sci-libs/io_lib/io_lib-1.9.0.ebuild b/sci-libs/io_lib/io_lib-1.9.0.ebuild
deleted file mode 100644
index 6a7ee600f540..000000000000
--- a/sci-libs/io_lib/io_lib-1.9.0.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/io_lib/io_lib-1.9.0.ebuild,v 1.1 2006/09/12 05:00:19 ribosome Exp $
-
-DESCRIPTION="A general purpose trace and experiment file reading/writing interface"
-HOMEPAGE="http://staden.sourceforge.net/"
-SRC_URI="mirror://sourceforge/staden/${P}.tar.bz2"
-LICENSE="staden"
-
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-
-S="${WORKDIR}/${PN}-1.9.0"
-
-src_compile() {
-	./configure --prefix=/usr \
-		--infodir=/usr/share/info \
-		--mandir=/usr/share/man || die
-
-	emake || die
-}
-
-src_install() {
-	make \
-		prefix=${D}/usr \
-		mandir=${D}/usr/share/man \
-		docdir=${D}/usr/share/doc/${PF} \
-		libdir=${D}/usr/lib \
-		infodir=${D}/usr/share/info \
-		install || die
-
-	dodoc CHANGES README
-}