Attachment 195047 Details for Bug 229693 – svn diff

[patch] svn diff

hmmer-3.2.1.diff (text/plain), 4.45 KB, created by Motomichi Matsuzaki on 2018-07-11 11:05:47 UTC

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Creator: Motomichi Matsuzaki

Created: 2018-07-11 11:05:47 UTC

Size: 4.45 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 474429)
>+++ Makefile	(working copy)
>@@ -2,31 +2,38 @@
> # $FreeBSD$
> 
> PORTNAME=	hmmer
>-PORTVERSION=	3.1b2
>+PORTVERSION=	3.2.1
> CATEGORIES=	biology
>-MASTER_SITES=	http://eddylab.org/software/hmmer3/${PORTVERSION}/
>+MASTER_SITES=	http://eddylab.org/software/hmmer/
> 
> MAINTAINER=	mzaki@niid.go.jp
> COMMENT=	Profile hidden Markov models for biological sequence analysis
> 
>-LICENSE=	GPLv3
>+LICENSE=	BSD3CLAUSE
> LICENSE_FILE=	${WRKSRC}/LICENSE
> 
>-USES=		gmake
>+ONLY_FOR_ARCHS=	amd64 i386 ia64 powerpc powerpc64
>+ONLY_FOR_ARCHS_REASON=	requires SSE2 or AltiVec instructions
>+
>+USES=		gmake perl5 shebangfix
>+
> GNU_CONFIGURE=	yes
> MAKE_ARGS=	V=1
> 
>+TEST_TARGET=	check
>+USE_PERL5=	test
>+SHEBANG_GLOB=	*.pl
>+SHEBANG_FILES=	easel/devkit/*
>+
> OPTIONS_DEFINE=	DOCS EXAMPLES TEST
>-TEST_TEST_TARGET=	check
>-TEST_USES=	shebangfix perl5
>-TEST_VARS=	shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build
> 
>-DOCFILES=	COPYRIGHT Userguide.pdf
>-EXAMPLES=	7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.out MADE1.sto \
>-		Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.out fn3.sto \
>-		globins4.hmm globins4.out globins4.sto globins45.fa \
>-		minifam minifam.h3f minifam.h3i minifam.h3m minifam.h3p
>+DOCFILES=	Userguide.pdf
>+EXAMPLES=	7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \
>+		Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.sto \
>+		globins4.hmm globins4.sto globins45.fa
> 
>+TEST_VARS=	use_perl5=build
>+
> post-build-TEST-on:	do-test
> 
> post-install:
>Index: distinfo
>===================================================================
>--- distinfo	(revision 474429)
>+++ distinfo	(working copy)
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1510218548
>-SHA256 (hmmer-3.1b2.tar.gz) = dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536
>-SIZE (hmmer-3.1b2.tar.gz) = 5965253
>+TIMESTAMP = 1531293655
>+SHA256 (hmmer-3.2.1.tar.gz) = a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c
>+SIZE (hmmer-3.2.1.tar.gz) = 7670274
>Index: files/patch-configure
>===================================================================
>--- files/patch-configure	(revision 474429)
>+++ files/patch-configure	(nonexistent)
>@@ -1,10 +0,0 @@
>---- configure.orig	2015-02-26 12:45:55 UTC
>-+++ configure
>-@@ -3912,6 +3912,7 @@ fi
>- if test "$impl_choice" = "none"; then
>-   case $host in
>-     ia64-*-*)      impl_choice=sse;;
>-+    amd64-*-*)     impl_choice=sse;;
>-     i?86-*-*)      impl_choice=sse;;
>-     x86*-*-*)      impl_choice=sse;;
>-     powerpc*-*-*)  impl_choice=vmx;;
>
>Property changes on: files/patch-configure
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 474429)
>+++ pkg-plist	(working copy)
>@@ -1,10 +1,8 @@
> bin/alimask
> bin/hmmalign
> bin/hmmbuild
>-bin/hmmc2
> bin/hmmconvert
> bin/hmmemit
>-bin/hmmerfm-exactmatch
> bin/hmmfetch
> bin/hmmlogo
> bin/hmmpgmd
>@@ -18,15 +16,6 @@
> bin/nhmmer
> bin/nhmmscan
> bin/phmmer
>-include/cachedb.h
>-include/hmmer.h
>-include/impl_sse.h
>-include/p7_config.h
>-include/p7_gbands.h
>-include/p7_gmxb.h
>-include/p7_gmxchk.h
>-include/p7_hmmcache.h
>-lib/libhmmer.a
> man/man1/alimask.1.gz
> man/man1/hmmalign.1.gz
> man/man1/hmmbuild.1.gz
>@@ -46,25 +35,16 @@
> man/man1/nhmmer.1.gz
> man/man1/nhmmscan.1.gz
> man/man1/phmmer.1.gz
>-%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
> %%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.hmm
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.out
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.sto
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dna_target.fa
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3f
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p

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Attachments on bug 229693: 195047