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| author |   Olivier Fisette <ribosome@gentoo.org> | 2005-03-25 17:40:02 +0000 |
|---|---|---|
| committer | Olivier Fisette <ribosome@gentoo.org> | 2005-03-25 17:40:02 +0000 |
| commit | 43ef74559a3e26c8862755c8b50aa351dddd660d (patch) | |
| tree | b7b91c68ed1bc8871720f15f87b8b6e468bee029 /sci-biology/embassy-domainatrix | |
| parent | Inherit multilib; support for Gentoo patches. (diff) | |
| download | historical-43ef74559a3e26c8862755c8b50aa351dddd660d.tar.gz historical-43ef74559a3e26c8862755c8b50aa351dddd660d.tar.bz2 historical-43ef74559a3e26c8862755c8b50aa351dddd660d.zip | |
Patched version for EMBOSS-2.10.
Package-Manager: portage-2.0.51.19
Diffstat (limited to 'sci-biology/embassy-domainatrix')
5 files changed, 73 insertions, 2 deletions
diff --git a/sci-biology/embassy-domainatrix/ChangeLog b/sci-biology/embassy-domainatrix/ChangeLog index a6f572ccbf0d..95f11da12c01 100644 --- a/sci-biology/embassy-domainatrix/ChangeLog +++ b/sci-biology/embassy-domainatrix/ChangeLog @@ -1,6 +1,13 @@ # 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 1.4 2005/03/02 23:30:04 j4rg0n Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.5 2005/03/25 17:40:02 ribosome Exp $ + +*embassy-domainatrix-1.0.0-r1 (25 Mar 2005) + + 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> + +files/embassy-domainatrix-1.0.0-r1.patch, + +embassy-domainatrix-1.0.0-r1.ebuild: + Patched version for EMBOSS-2.10. 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-domainatrix-1.0.0.ebuild: diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest index 7212d0b60158..7d79889cedb2 100644 --- a/sci-biology/embassy-domainatrix/Manifest +++ b/sci-biology/embassy-domainatrix/Manifest @@ -1,4 +1,7 @@ MD5 a0604f115c3531ac9c9beb314c8f3af7 embassy-domainatrix-1.0.0.ebuild 361 -MD5 d6247fc6e8014b4df7260cd93d47e59a ChangeLog 1040 +MD5 55b31178f283aba77383fcaafe91a599 embassy-domainatrix-1.0.0-r1.ebuild 367 +MD5 687878ed351c58166349dd0d1f6bb07f ChangeLog 1261 MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254 MD5 2cfc7dc10348dc74cffc22396f14c678 files/digest-embassy-domainatrix-1.0.0 135 +MD5 b19c37b0a72a2de514b159fb5906937d files/embassy-domainatrix-1.0.0-r1.patch 1965 +MD5 85379661fddfc18d2311bd60dde35ee9 files/digest-embassy-domainatrix-1.0.0-r1 136 diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-1.0.0-r1.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-1.0.0-r1.ebuild new file mode 100644 index 000000000000..20b422b55784 --- /dev/null +++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-1.0.0-r1.ebuild @@ -0,0 +1,9 @@ +# 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 1.1 2005/03/25 17:40:02 ribosome Exp $ + +inherit embassy-2.10 + +DESCRIPTION="Protein 3D analysis add-on package for EMBOSS" + +KEYWORDS="~x86 ~ppc ~ppc-macos" diff --git a/sci-biology/embassy-domainatrix/files/digest-embassy-domainatrix-1.0.0-r1 b/sci-biology/embassy-domainatrix/files/digest-embassy-domainatrix-1.0.0-r1 new file mode 100644 index 000000000000..d48048232a0a --- /dev/null +++ b/sci-biology/embassy-domainatrix/files/digest-embassy-domainatrix-1.0.0-r1 @@ -0,0 +1,2 @@ +MD5 4a48388ced7021a8ffece5166c40a364 EMBOSS-2.10.0.tar.gz 16262124 +MD5 78e1145851073a277e568ee3a691d999 DOMAINATRIX-1.0.0.tar.gz 551090 diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-1.0.0-r1.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-1.0.0-r1.patch new file mode 100644 index 000000000000..21e54040e999 --- /dev/null +++ b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-1.0.0-r1.patch @@ -0,0 +1,50 @@ +--- 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); |