# ChangeLog for sci-biology/embassy-domainatrix
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.13 2005/10/03 23:54:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.14 2005/10/04 00:06:30 ribosome Exp $
+
+ 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+ -files/embassy-domainatrix-1.0.0-r1.patch,
+ -embassy-domainatrix-1.0.0-r1.ebuild:
+ Removed obsolete version.
03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
embassy-domainatrix-0.1.0.ebuild:
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/embassy-domainatrix-1.0.0-r1.ebuild,v 1.5 2005/08/07 21:41:10 ribosome Exp $
-
-EBOV="2.10.0"
-
-inherit embassy
-
-DESCRIPTION="Protein domain analysis add-on package for EMBOSS"
-
-KEYWORDS="ppc ppc-macos x86"
+++ /dev/null
-MD5 4a48388ced7021a8ffece5166c40a364 EMBOSS-2.10.0.tar.gz 16262124
-MD5 78e1145851073a277e568ee3a691d999 DOMAINATRIX-1.0.0.tar.gz 551090
+++ /dev/null
---- src/pdbparse.c.old 2005-03-25 12:12:50.000000000 -0500
-+++ src/pdbparse.c 2005-03-25 10:55:57.000000000 -0500
-@@ -240,7 +240,7 @@
-
- /* Parse pdb file and write pdb structure */
- if(!(pdb=ajPdbReadRawNew(pdb_inf, pdbid, min_chain_size, max_mismatch,
-- camask, camask1, atommask, logf)))
-+ 0, camask, camask1, atommask, logf)))
- {
- ajFmtPrintS(&msg, "Clean coordinate file not generated for %S", temp);
- ajWarn(ajStrStr(msg));
---- src/scopnr.c.old 2005-03-25 12:17:40.000000000 -0500
-+++ src/scopnr.c 2005-03-25 11:11:28.000000000 -0500
-@@ -324,10 +324,10 @@
- /* Remove redundancy from list_seqs*/
- if(moden==1)
- ret=embDmxSeqNR(list_seqs, &keep, &nsetnr, matrix, gapopen,
-- gapextend,thresh);
-+ gapextend,thresh, FALSE);
- else
- ret=embDmxSeqNRRange(list_seqs, &keep, &nsetnr, matrix, gapopen,
-- gapextend,threshlow, threshup);
-+ gapextend,threshlow, threshup, FALSE);
- if(!ret)
- {
- ajStrDel(&last_fam);
-@@ -464,10 +464,10 @@
- /* Remove redundancy from list_seqs*/
- if(moden==1)
- embDmxSeqNR(list_seqs, &keep, &nsetnr, matrix, gapopen,
-- gapextend,thresh);
-+ gapextend,thresh, FALSE);
- else
- embDmxSeqNRRange(list_seqs, &keep, &nsetnr, matrix, gapopen,
-- gapextend,threshlow, threshup);
-+ gapextend,threshlow, threshup, FALSE);
-
- /* Write file with SCOP entries that are retained*/
- for(iter=ajListIterRead(list_scop), x=0;
---- src/seqnr.c.old 2005-03-25 12:19:34.000000000 -0500
-+++ src/seqnr.c 2005-03-25 11:13:42.000000000 -0500
-@@ -829,7 +829,7 @@
-
- /* Remove the redundancy from the sequence set */
- /*JISON*/ keep = ajIntNew();
-- embDmxSeqNR(famin_seqs, &keep, &nsetnr, matrix, gapopen, gapextend, thresh);
-+ embDmxSeqNR(famin_seqs, &keep, &nsetnr, matrix, gapopen, gapextend, thresh, FALSE);
-
- /* clean up famin_seqs */
- iter=ajListIterRead(famin_seqs);
# ChangeLog for sci-biology/embassy-emnu
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.13 2005/10/03 23:54:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.14 2005/10/04 00:06:30 ribosome Exp $
+
+ 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+ -files/embassy-emnu-1.05-r1.patch, -embassy-emnu-1.05-r1.ebuild:
+ Removed obsolete version.
03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
embassy-emnu-1.05-r2.ebuild:
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/embassy-emnu-1.05-r1.ebuild,v 1.5 2005/08/07 21:41:10 ribosome Exp $
-
-EBOV="2.10.0"
-
-inherit embassy
-
-DESCRIPTION="EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications"
-
-KEYWORDS="ppc ppc-macos x86"
-
-RDEPEND="sys-libs/ncurses
- ${RDEPEND}"
-
-DEPEND="sys-libs/ncurses
- ${DEPEND}"
+++ /dev/null
-MD5 4a48388ced7021a8ffece5166c40a364 EMBOSS-2.10.0.tar.gz 16262124
-MD5 81435e71026a8ae6c361831a38ec1662 EMNU-1.05.tar.gz 340031
+++ /dev/null
---- source/emnu.c.old 2005-03-25 12:28:08.000000000 -0500
-+++ source/emnu.c 2005-03-25 11:33:23.000000000 -0500
-@@ -3080,7 +3080,7 @@
- ** don't want to ignore applications that don't work in GUIs
- ** (emnu is not a GUI!)
- */
-- embGrpGetProgGroups (glist, alpha, env, ajTrue, ajTrue, explode,
-+ embGrpGetProgGroups (glist, alpha, env, ajTrue, ajTrue, NULL, explode,
- ajFalse, ajFalse);
-
-
# ChangeLog for sci-biology/embassy-esim4
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.13 2005/10/03 23:54:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.14 2005/10/04 00:06:30 ribosome Exp $
+
+ 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+ -embassy-esim4-1.0.0-r1.ebuild:
+ Removed obsolete version.
03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
embassy-esim4-1.0.0-r2.ebuild:
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r1.ebuild,v 1.5 2005/08/07 21:41:10 ribosome Exp $
-
-EBOV="2.10.0"
-
-inherit embassy
-
-DESCRIPTION="EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA"
-
-KEYWORDS="ppc ppc-macos x86"
+++ /dev/null
-MD5 4a48388ced7021a8ffece5166c40a364 EMBOSS-2.10.0.tar.gz 16262124
-MD5 d00209b958a45a1ba7cb617950e3fa48 ESIM4-1.0.0.tar.gz 375473
# ChangeLog for sci-biology/embassy-hmmer
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.14 2005/10/03 23:54:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.15 2005/10/04 00:06:31 ribosome Exp $
+
+ 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+ -embassy-hmmer-2.1.1-r1.ebuild:
+ Removed obsolete version.
03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
embassy-hmmer-2.1.1-r2.ebuild:
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/embassy-hmmer-2.1.1-r1.ebuild,v 1.6 2005/08/07 21:41:10 ribosome Exp $
-
-EBOV="2.10.0"
-
-inherit embassy
-
-DESCRIPTION="EMBOSS integrated version of HMMER - Biological sequence analysis with profile HMMs"
-
-KEYWORDS="ppc ppc-macos x86"
-
-src_install() {
- embassy_src_install
- insinto /usr/include/emboss/hmmer
- doins src/*.h
-}
+++ /dev/null
-MD5 4a48388ced7021a8ffece5166c40a364 EMBOSS-2.10.0.tar.gz 16262124
-MD5 e060f31a25074dd64a7885a85cbc15da HMMER-2.1.1.tar.gz 552322
# ChangeLog for sci-biology/embassy-meme
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/ChangeLog,v 1.14 2005/10/03 23:54:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/ChangeLog,v 1.15 2005/10/04 00:06:31 ribosome Exp $
+
+ 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+ -embassy-meme-2.3.1-r1.ebuild:
+ Removed obsolete version.
03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
embassy-meme-2.3.1-r2.ebuild:
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-meme/embassy-meme-2.3.1-r1.ebuild,v 1.6 2005/08/07 21:41:10 ribosome Exp $
-
-EBOV="2.10.0"
-
-inherit embassy
-
-DESCRIPTION="EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation"
-
-KEYWORDS="ppc ppc-macos x86"
-
-src_install() {
- embassy_src_install
- insinto /usr/include/emboss/meme
- doins src/INCLUDE/*.h
-}
+++ /dev/null
-MD5 4a48388ced7021a8ffece5166c40a364 EMBOSS-2.10.0.tar.gz 16262124
-MD5 f81f0a6fffcd202e577b25085037bb5e MEME-2.3.1.tar.gz 415122
# ChangeLog for sci-biology/embassy-mse
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.14 2005/10/03 23:54:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.15 2005/10/04 00:06:31 ribosome Exp $
+
+ 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+ -embassy-mse-1.0.0-r1.ebuild:
+ Removed obsolete version.
03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
embassy-mse-1.0.0-r2.ebuild:
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/embassy-mse-1.0.0-r1.ebuild,v 1.6 2005/08/07 21:41:10 ribosome Exp $
-
-EBOV="2.10.0"
-
-inherit embassy
-
-DESCRIPTION="EMBOSS integrated version of MSE - Multiple Sequence Editor"
-
-KEYWORDS="ppc ppc-macos x86"
-
-src_install() {
- embassy_src_install
- insinto /usr/include/emboss/mse
- doins h/*.h
-}
+++ /dev/null
-MD5 4a48388ced7021a8ffece5166c40a364 EMBOSS-2.10.0.tar.gz 16262124
-MD5 c599e848a44d6353e42fb59578417e41 MSE-1.0.0.tar.gz 405440
# ChangeLog for sci-biology/embassy-phylip
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylip/ChangeLog,v 1.14 2005/10/03 23:54:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylip/ChangeLog,v 1.15 2005/10/04 00:06:31 ribosome Exp $
+
+ 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+ -embassy-phylip-3.57c-r1.ebuild:
+ Removed obsolete version.
03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
embassy-phylip-3.6b.ebuild:
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylip/embassy-phylip-3.57c-r1.ebuild,v 1.5 2005/08/07 21:41:10 ribosome Exp $
-
-EBOV="2.10.0"
-
-inherit embassy
-
-DESCRIPTION="EMBOSS integrated version of the PHYLogeny Inference Package"
-LICENSE="freedist"
-
-KEYWORDS="ppc ppc-macos x86"
+++ /dev/null
-MD5 4a48388ced7021a8ffece5166c40a364 EMBOSS-2.10.0.tar.gz 16262124
-MD5 6a5afaed10f177758b84f2c3c51aee78 PHYLIP-3.57c.tar.gz 843060
# ChangeLog for sci-biology/embassy-topo
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.13 2005/10/03 23:54:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.14 2005/10/04 00:06:31 ribosome Exp $
+
+ 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
+ -embassy-topo-1.0.0-r1.ebuild:
+ Removed obsolete version.
03 Oct 2005; Olivier Fisette <ribosome@gentoo.org>
embassy-topo-1.0.0-r2.ebuild:
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/embassy-topo-1.0.0-r1.ebuild,v 1.5 2005/08/07 21:41:11 ribosome Exp $
-
-EBOV="2.10.0"
-
-inherit embassy
-
-DESCRIPTION="EMBOSS integrated version of TOPO - Transmembrane protein display"
-
-KEYWORDS="ppc ppc-macos x86"
+++ /dev/null
-MD5 4a48388ced7021a8ffece5166c40a364 EMBOSS-2.10.0.tar.gz 16262124
-MD5 51885b65b79b87631f3536362e453ed8 TOPO-1.0.0.tar.gz 342704
# ChangeLog for sci-biology/embassy
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.17 2005/10/03 23:54:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.18 2005/10/04 00:06:30 ribosome Exp $
+
+ 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -embassy-2.10.0.ebuild:
+ Removed obsolete version.
03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> embassy-3.0.0.ebuild:
Stable on ppc-macos (with j4rg0n's permission, bug #102420).
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/embassy-2.10.0.ebuild,v 1.7 2005/07/27 05:10:54 j4rg0n Exp $
-
-DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)"
-HOMEPAGE="http://www.emboss.org/"
-SRC_URI=""
-LICENSE="GPL-2 freedist"
-
-SLOT="0"
-KEYWORDS="ppc ppc-macos x86"
-IUSE=""
-
-# IUSE="no-conflict"
-# In the future, I plan to integrate packages such as the standalone meme, which
-# would conflict with the corresponding embassy-meme package. Conflicting
-# EMBASSY packages will be marked as blockers of the standalone version (and vice
-# versa), and the no-conflict USE flag will make it easy to install all EMBASSY
-# packages except the conflictual ones.
-
-RDEPEND="!=sci-biology/emboss-2.9*
- =sci-biology/emboss-2.10*
- =sci-biology/embassy-construct-1.0.0
- =sci-biology/embassy-domainatrix-1.0.0-r1
- =sci-biology/embassy-emnu-1.05-r1
- =sci-biology/embassy-esim4-1.0.0-r1
- =sci-biology/embassy-hmmer-2.1.1-r1
- =sci-biology/embassy-meme-2.3.1-r1
- =sci-biology/embassy-mse-1.0.0-r1
- =sci-biology/embassy-phylip-3.57c-r1
- =sci-biology/embassy-topo-1.0.0-r1"
projects / gentoo.git / commitdiff