Attachment 211100 Details for Bug 243247 – svn diff for biology/infernal to 1.1.3 (revised)

[patch] svn diff for biology/infernal to 1.1.3 (revised)

infernal-1.1.3.diff (text/plain), 5.64 KB, created by Motomichi Matsuzaki on 2020-01-27 09:56:38 UTC

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Creator: Motomichi Matsuzaki

Created: 2020-01-27 09:56:38 UTC

Size: 5.64 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 522566)
>+++ Makefile	(working copy)
>@@ -1,23 +1,31 @@
> # $FreeBSD$
> 
> PORTNAME=	infernal
>-PORTVERSION=	1.1.2
>+PORTVERSION=	1.1.3
> CATEGORIES=	biology
> MASTER_SITES=	http://eddylab.org/infernal/
> 
>-MAINTAINER=	mzaki@niid.go.jp
>+MAINTAINER=	mzaki@e-mail.ne.jp
> COMMENT=	Search sequence databases for structural RNA homologs
> 
> LICENSE=	BSD3CLAUSE
> LICENSE_FILE=	${WRKSRC}/LICENSE
> 
>-ONLY_FOR_ARCHS=	amd64 i386 powerpc64
>+ONLY_FOR_ARCHS=	amd64 i386 powerpc powerpc64 powerpcspe
> ONLY_FOR_ARCHS_REASON=	requires SSE2 or AltiVec instructions
> 
>-USES=		gmake
>+USES=		compiler:c11 gmake perl5 python:3.5+,test shebangfix
>+
> GNU_CONFIGURE=	yes
> MAKE_ARGS=	V=1
> 
>+TEST_TARGET=	check
>+USE_PERL5=	test
>+SHEBANG_GLOB=	*.pl *.py
>+SHEBANG_FILES=	easel/devkit/*
>+
>+OPTIONS_DEFINE=	DOCS EXAMPLES TEST
>+
> DOCFILES=	Userguide.pdf
> EXAMPLES=	5S_rRNA.c.cm 5S_rRNA.sto \
> 		Cobalamin.c.cm Cobalamin.fa Cobalamin.sto \
>@@ -27,14 +35,17 @@
> 		tRNA5-hand.c.cm tRNA5-hand.sto tRNA5-mrum.out \
> 		tRNA5-noss.sto tRNA5.c.cm tRNA5.sto
> 
>-OPTIONS_DEFINE=	DOCS EXAMPLES TEST
>+TEST_VARS=	use_perl5=build
>+TEST_BUILD_DEPENDS=	${PYTHON_VERSION}:lang/python${PYTHON_SUFFIX}
> 
>-TEST_TEST_TARGET=	check
>-TEST_USES=	shebangfix perl5
>-TEST_VARS=	shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build
>+post-build-TEST-on:	pre-test do-test
> 
>-post-build-TEST-on:	do-test
>+pre-test:
>+	${FIND} ${WRKSRC} -type f $ -name Makefile -or -name sqc $ -exec ${GREP} -q 'python3 ' {} \; -print | ${XARGS} ${SED} -i.bak 's/python3 /${PYTHON_VERSION} /'
> 
>+post-install:
>+	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*
>+
> post-install-DOCS-on:
> 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
> 	${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR}
>Index: distinfo
>===================================================================
>--- distinfo	(revision 522566)
>+++ distinfo	(working copy)
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1528251928
>-SHA256 (infernal-1.1.2.tar.gz) = ac8c24f484205cfb7124c38d6dc638a28f2b9035b9433efec5dc753c7e84226b
>-SIZE (infernal-1.1.2.tar.gz) = 19364073
>+TIMESTAMP = 1578660730
>+SHA256 (infernal-1.1.3.tar.gz) = 3b98a6a3a0e7b01aa077a0caf1e958223c4d8f80a69a4eb602ca59a3475da85e
>+SIZE (infernal-1.1.3.tar.gz) = 29910035
>Index: files/patch-configure
>===================================================================
>--- files/patch-configure	(revision 522566)
>+++ files/patch-configure	(nonexistent)
>@@ -1,10 +0,0 @@
>---- configure.orig	2016-07-01 20:26:34 UTC
>-+++ configure
>-@@ -3855,6 +3855,7 @@ 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 ##
>-on
>\ 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: files/patch-hmmer_src_hmmc2.c
>===================================================================
>--- files/patch-hmmer_src_hmmc2.c	(nonexistent)
>+++ files/patch-hmmer_src_hmmc2.c	(working copy)
>@@ -0,0 +1,11 @@
>+--- hmmer/src/hmmc2.c.orig	2019-11-19 19:30:04 UTC
>++++ hmmer/src/hmmc2.c
>+@@ -334,7 +334,7 @@ int main(int argc, char *argv[])
>+       n = sizeof(sstatus);
>+       total += n;
>+       if ((size = readn(sock, &sstatus, n)) == -1) {
>+-        if(errno == 104 || errno == 0){
>++        if(errno == ECONNRESET || errno == 0){
>+           // connection was reset, usually because server exited
>+           fprintf(stderr, "Daemon exited, shutting down\n");
>+           exit(0);
>
>Property changes on: files/patch-hmmer_src_hmmc2.c
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property
>Index: files/patch-src_Makefile.in
>===================================================================
>--- files/patch-src_Makefile.in	(nonexistent)
>+++ files/patch-src_Makefile.in	(working copy)
>@@ -0,0 +1,19 @@
>+--- src/Makefile.in.orig	2019-11-19 19:28:55 UTC
>++++ src/Makefile.in
>+@@ -27,6 +27,7 @@ CC             = @CC@
>+ CFLAGS         = @CFLAGS@
>+ PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ 
>+ PIC_CFLAGS     = @PIC_CFLAGS@
>++SIMD_CFLAGS    = @SSE_CFLAGS@ @VMX_CFLAGS@
>+ CPPFLAGS       = @CPPFLAGS@
>+ LDFLAGS        = @LDFLAGS@
>+ DEFS           = @DEFS@
>+@@ -200,7 +201,7 @@ ${PROGS}: % : %.o libinfernal.a ../${HMM
>+ 	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
>+ 
>+ .c.o:
>+-	${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $<
>++	${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $<
>+ 
>+ ${ITESTS}: % : %.o libinfernal.a ../${HMMERDIR}/src/libhmmer.a ../${ESLDIR}/libeasel.a ${HDRS} config.h
>+ 	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
>
>Property changes on: files/patch-src_Makefile.in
>___________________________________________________________________
>Added: fbsd:nokeywords
>## -0,0 +1 ##
>+yes
>\ No newline at end of property
>Added: svn:eol-style
>## -0,0 +1 ##
>+native
>\ No newline at end of property
>Added: svn:mime-type
>## -0,0 +1 ##
>+text/plain
>\ No newline at end of property

Flags:

mzaki: maintainer-approval+

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Attachments on bug 243247: 210595 | 210784 | 211100