FreeBSD Bugzilla – Attachment 210595 Details for
Bug 243247
biology/infernal: Update to 1.1.3
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[patch]
svn diff for biology/infernal to 1.1.3
infernal-1.1.3.diff (text/plain), 4.62 KB, created by
Motomichi Matsuzaki
on 2020-01-10 14:25:00 UTC
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Description:
svn diff for biology/infernal to 1.1.3
Filename:
MIME Type:
Creator:
Motomichi Matsuzaki
Created:
2020-01-10 14:25:00 UTC
Size:
4.62 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-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
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