From 61a2735ae5b4dd418adb2e38203093bae8fd813d Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Sun, 10 Dec 2006 19:04:53 +0000 Subject: [PATCH] Removing sci-biology/cbcanalyzer from Portage (see bug #153881) --- sci-biology/cbcanalyzer/ChangeLog | 22 ------------- sci-biology/cbcanalyzer/Manifest | 24 -------------- .../cbcanalyzer/cbcanalyzer-1.0.0.ebuild | 31 ------------------- .../cbcanalyzer/cbcanalyzer-1.0.2.ebuild | 31 ------------------- .../files/digest-cbcanalyzer-1.0.0 | 1 - .../files/digest-cbcanalyzer-1.0.2 | 1 - sci-biology/cbcanalyzer/metadata.xml | 27 ---------------- 7 files changed, 137 deletions(-) delete mode 100644 sci-biology/cbcanalyzer/ChangeLog delete mode 100644 sci-biology/cbcanalyzer/Manifest delete mode 100644 sci-biology/cbcanalyzer/cbcanalyzer-1.0.0.ebuild delete mode 100644 sci-biology/cbcanalyzer/cbcanalyzer-1.0.2.ebuild delete mode 100644 sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.0 delete mode 100644 sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.2 delete mode 100644 sci-biology/cbcanalyzer/metadata.xml diff --git a/sci-biology/cbcanalyzer/ChangeLog b/sci-biology/cbcanalyzer/ChangeLog deleted file mode 100644 index 5b8e9e776250..000000000000 --- a/sci-biology/cbcanalyzer/ChangeLog +++ /dev/null @@ -1,22 +0,0 @@ -# ChangeLog for sci-biology/cbcanalyzer -# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/cbcanalyzer/ChangeLog,v 1.4 2005/07/05 09:54:40 dholm Exp $ - - 05 Jul 2005; David Holm cbcanalyzer-1.0.2.ebuild: - Added to ~ppc. - -*cbcanalyzer-1.0.2 (04 Jul 2005) - - 04 Jul 2005; Andreas Pokorny +cbcanalyzer-1.0.2.ebuild: - New version, with several bug fixes and minor feature additions. - - 04 Jul 2005; Andreas Pokorny cbcanalyzer-1.0.0.ebuild: - Changed the SRC_URI and HOMEPAGE - - -*cbcanalyzer-1.0.0 (25 Apr 2005) - - 25 Apr 2005; Andreas Pokorny - cbcanalyzer-1.0.0.ebuild, ChangeLog, metadata.xml: - Initial import - diff --git a/sci-biology/cbcanalyzer/Manifest b/sci-biology/cbcanalyzer/Manifest deleted file mode 100644 index 48995c724e13..000000000000 --- a/sci-biology/cbcanalyzer/Manifest +++ /dev/null @@ -1,24 +0,0 @@ -DIST cbcanalyzer-1.0.0.tar.gz 1729756 -DIST cbcanalyzer-1.0.2.tar.gz 1737660 -EBUILD cbcanalyzer-1.0.0.ebuild 880 RMD160 5057d55a9230082b32c5cd0b34d3c6b8a4c8d855 SHA1 3769a0d24fbfb68247cc5cb788394c55ee800169 SHA256 d7d8e92dfb08bed8fe7d8e0213a59eb875cdca2daa06df666600caa68903206c -MD5 b2707fec7fb6f02210820b71a7ca6bc0 cbcanalyzer-1.0.0.ebuild 880 -RMD160 5057d55a9230082b32c5cd0b34d3c6b8a4c8d855 cbcanalyzer-1.0.0.ebuild 880 -SHA256 d7d8e92dfb08bed8fe7d8e0213a59eb875cdca2daa06df666600caa68903206c cbcanalyzer-1.0.0.ebuild 880 -EBUILD cbcanalyzer-1.0.2.ebuild 882 RMD160 b3dd16626f8bb1ead7f9cbb1040fb19316b50393 SHA1 2b10d57b1baf90b535d3778bae03ea685a02187b SHA256 206da3c15e0728e664f199e37bc7f3bd665a8e265d0c36fc1476dcd81977f820 -MD5 e675e183246a2227a0f7265c1b7c7771 cbcanalyzer-1.0.2.ebuild 882 -RMD160 b3dd16626f8bb1ead7f9cbb1040fb19316b50393 cbcanalyzer-1.0.2.ebuild 882 -SHA256 206da3c15e0728e664f199e37bc7f3bd665a8e265d0c36fc1476dcd81977f820 cbcanalyzer-1.0.2.ebuild 882 -MISC ChangeLog 766 RMD160 62f30d4784b881f0b15cf93642d931baffb91f81 SHA1 a91e2c08530dd78ac7bf34fcce8ffb230f934dc8 SHA256 95905d7811c8321f0de6bfbdd8c6d981dc3ac0fd8e316e57a3360c2d99fb07bf -MD5 ca86d7602abc53c0510c68fcfa6fe0e8 ChangeLog 766 -RMD160 62f30d4784b881f0b15cf93642d931baffb91f81 ChangeLog 766 -SHA256 95905d7811c8321f0de6bfbdd8c6d981dc3ac0fd8e316e57a3360c2d99fb07bf ChangeLog 766 -MISC metadata.xml 1525 RMD160 bfe724d402979a39e8843a9d48c9eca1d577e5fe SHA1 867024d583fe01e9dba5edef716a248103204002 SHA256 ea33690a6c0e163a489b0e168d0aebe94930897c392c750b5e906d9c551b5d83 -MD5 e720abed57e2a1a5d8ae0b7bf7151d01 metadata.xml 1525 -RMD160 bfe724d402979a39e8843a9d48c9eca1d577e5fe metadata.xml 1525 -SHA256 ea33690a6c0e163a489b0e168d0aebe94930897c392c750b5e906d9c551b5d83 metadata.xml 1525 -MD5 f69a329aa4d9ac75cae676a247c6fa52 files/digest-cbcanalyzer-1.0.0 70 -RMD160 049cd1b290701533f86f5b291ea57c52c54975e4 files/digest-cbcanalyzer-1.0.0 70 -SHA256 acd0ba8158d77b91da8e7cc99d1b9c454c77dd899689ae7f37f7fa216a00cab6 files/digest-cbcanalyzer-1.0.0 70 -MD5 42785cbb5761aa74eb0f4721aaf83aa3 files/digest-cbcanalyzer-1.0.2 70 -RMD160 65b76dfb7ed0975a1fbb150554de3de612534e9f files/digest-cbcanalyzer-1.0.2 70 -SHA256 735718722115d632028edf74425c1f85f32542056ac91b76352a917417ab4af7 files/digest-cbcanalyzer-1.0.2 70 diff --git a/sci-biology/cbcanalyzer/cbcanalyzer-1.0.0.ebuild b/sci-biology/cbcanalyzer/cbcanalyzer-1.0.0.ebuild deleted file mode 100644 index 15f17358ec52..000000000000 --- a/sci-biology/cbcanalyzer/cbcanalyzer-1.0.0.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/cbcanalyzer/cbcanalyzer-1.0.0.ebuild,v 1.2 2005/07/04 19:24:16 apokorny Exp $ - -DESCRIPTION="Creates phylogenetic trees measuring compensatory base changes" -HOMEPAGE="http://www.biozentrum.uni-wuerzburg.de/index.php?id=524" -SRC_URI="http://www.biozentrum.uni-wuerzburg.de/fileadmin/user_upload/bioinformatik/${P}.tar.gz" -LICENSE="GPL-2" - -KEYWORDS="~amd64 ~x86" -SLOT="0" -IUSE="" - -DEPEND=">=x11-libs/wxGTK-2.4.2 - >=dev-libs/boost-1.32-r1" - - -# cbcanalyzer works with wxGTK-2.4/wxGTK-2.5 gtk1 gtk2 -# but only the non unicode versions - -src_install() { - make install DESTDIR=${D} || die -} - -pkg_postinst() { - einfo - einfo "To visualize trees you might want to install sci-biology/njplot" - einfo "and sci-biology/treeviewx." - einfo -} - diff --git a/sci-biology/cbcanalyzer/cbcanalyzer-1.0.2.ebuild b/sci-biology/cbcanalyzer/cbcanalyzer-1.0.2.ebuild deleted file mode 100644 index f0d8f29334d8..000000000000 --- a/sci-biology/cbcanalyzer/cbcanalyzer-1.0.2.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2005 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/cbcanalyzer/cbcanalyzer-1.0.2.ebuild,v 1.2 2005/07/05 09:54:40 dholm Exp $ - -DESCRIPTION="Creates phylogenetic trees measuring compensatory base changes" -HOMEPAGE="http://www.biozentrum.uni-wuerzburg.de/index.php?id=524" -SRC_URI="http://www.biozentrum.uni-wuerzburg.de/fileadmin/user_upload/bioinformatik/${P}.tar.gz" -LICENSE="GPL-2" - -KEYWORDS="~amd64 ~ppc ~x86" -SLOT="0" -IUSE="" - -DEPEND=">=x11-libs/wxGTK-2.4.2 - >=dev-libs/boost-1.32-r1" - - -# cbcanalyzer works with wxGTK-2.4/wxGTK-2.5 gtk1 gtk2 -# but only the non unicode versions - -src_install() { - make install DESTDIR=${D} || die -} - -pkg_postinst() { - einfo - einfo "To visualize trees you might want to install sci-biology/njplot" - einfo "and sci-biology/treeviewx." - einfo -} - diff --git a/sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.0 b/sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.0 deleted file mode 100644 index c1fd3fa395ba..000000000000 --- a/sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.0 +++ /dev/null @@ -1 +0,0 @@ -MD5 8ad9c083dd80bab335a2a4cf6b7397a9 cbcanalyzer-1.0.0.tar.gz 1729756 diff --git a/sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.2 b/sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.2 deleted file mode 100644 index 3fae98d8c7f3..000000000000 --- a/sci-biology/cbcanalyzer/files/digest-cbcanalyzer-1.0.2 +++ /dev/null @@ -1 +0,0 @@ -MD5 f7ffcf588b37e5270e9df8015da9a3d6 cbcanalyzer-1.0.2.tar.gz 1737660 diff --git a/sci-biology/cbcanalyzer/metadata.xml b/sci-biology/cbcanalyzer/metadata.xml deleted file mode 100644 index a24885e7c24c..000000000000 --- a/sci-biology/cbcanalyzer/metadata.xml +++ /dev/null @@ -1,27 +0,0 @@ - - - - sci-biology - - CBCAnalyzer reads several CT-file formats (ct, RNAviz ct or Mac ct), - and generates a so called ``bracket-dot-bracket'' format that typically - is used as input for other tools such as RNAforester, RNAmovie or - MARNA. The latter one creates a multiple alignment based on primary - sequences and secondary structures that now can be used as input for - CBCDetect. CBCAnalyzer counts compensatory base changes in all against all - of the aligned sequences. - The count (distance) matrix obtained by CBCDetect is used as input - for CBCTree that reconstructs a phylogram by using the algorithm of BIONJ. - - - CBCAnalyzer liest unterschiedliche CT-Format (ct, RNAviz ct oder Mac ct), - und generiert daraus ein sogenanntes ``Klammer-Punkt-Klammer'' Format, dass - normalerweise als Eingabe für Programme wie RNAforester, RNAmovie oder - MARNA dient. Letzteres erzeugt ein multiples Aligment primaer basierend auf der - Sequenz und sekundär basierend auf der Struktur, dies als Eingabe für - CBCDetect verwendet werden. CBCAnalyzer zählt dann kompensierende - Basiswechsel in allen Sequenzen. - Diese Zähl oder Distanzmatrix aus CBCDetect wird als Eingabe für CBCTree - verwendet, um ein Phylogram mit Hilfe des BIONJ-Algorithmus zu erzeugen. - - -- 2.26.2