Date: Wed, 12 Oct 2022 10:16:06 GMT From: Nuno Teixeira <eduardo@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 95b2e3a08855 - main - biology/infernal: Update to 1.1.4 Message-ID: <202210121016.29CAG6fT019885@gitrepo.freebsd.org>
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The branch main has been updated by eduardo: URL: https://cgit.FreeBSD.org/ports/commit/?id=95b2e3a08855793600b2587fc598eb23ef83f388 commit 95b2e3a08855793600b2587fc598eb23ef83f388 Author: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> AuthorDate: 2022-10-12 10:06:23 +0000 Commit: Nuno Teixeira <eduardo@FreeBSD.org> CommitDate: 2022-10-12 10:15:54 +0000 biology/infernal: Update to 1.1.4 ChangeLog: http://eddylab.org/infernal/RELEASE-1.1.4.md PR: 266967 --- biology/infernal/Makefile | 16 ++++++++-------- biology/infernal/distinfo | 6 +++--- biology/infernal/files/patch-hmmer_src_hmmc2.c | 11 ----------- biology/infernal/files/patch-src_Makefile.in | 19 ------------------- 4 files changed, 11 insertions(+), 41 deletions(-) diff --git a/biology/infernal/Makefile b/biology/infernal/Makefile index 528494dbb63a..af7f5630d313 100644 --- a/biology/infernal/Makefile +++ b/biology/infernal/Makefile @@ -1,5 +1,5 @@ PORTNAME= infernal -PORTVERSION= 1.1.3 +PORTVERSION= 1.1.4 CATEGORIES= biology MASTER_SITES= http://eddylab.org/infernal/ @@ -14,14 +14,14 @@ ONLY_FOR_ARCHS= amd64 i386 powerpc powerpc64 powerpc64le powerpcspe ONLY_FOR_ARCHS_REASON= requires SSE2 or AltiVec instructions USES= compiler:c11 gmake perl5 python:3.5+,test shebangfix +USE_PERL5= test +SHEBANG_FILES= easel/devkit/* +SHEBANG_GLOB= *.pl *.py 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 @@ -34,14 +34,11 @@ EXAMPLES= 5S_rRNA.c.cm 5S_rRNA.sto \ tRNA5-hand.c.cm tRNA5-hand.sto tRNA5-mrum.out \ tRNA5-noss.sto tRNA5.c.cm tRNA5.sto -TEST_VARS= use_perl5=build TEST_BUILD_DEPENDS= ${PYTHON_VERSION}:lang/python${PYTHON_SUFFIX} +TEST_VARS= use_perl5=build post-build-TEST-on: pre-test 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/* @@ -53,4 +50,7 @@ post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR} +pre-test: + ${FIND} ${WRKSRC} -type f \( -name Makefile -or -name sqc \) -exec ${GREP} -q 'python3 ' {} \; -print | ${XARGS} ${SED} -i.bak 's/python3 /${PYTHON_VERSION} /' + .include <bsd.port.mk> diff --git a/biology/infernal/distinfo b/biology/infernal/distinfo index 9f362448abc8..80865c942e66 100644 --- a/biology/infernal/distinfo +++ b/biology/infernal/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1578660730 -SHA256 (infernal-1.1.3.tar.gz) = 3b98a6a3a0e7b01aa077a0caf1e958223c4d8f80a69a4eb602ca59a3475da85e -SIZE (infernal-1.1.3.tar.gz) = 29910035 +TIMESTAMP = 1665487539 +SHA256 (infernal-1.1.4.tar.gz) = f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc +SIZE (infernal-1.1.4.tar.gz) = 29499238 diff --git a/biology/infernal/files/patch-hmmer_src_hmmc2.c b/biology/infernal/files/patch-hmmer_src_hmmc2.c deleted file mode 100644 index 5bd86cf55247..000000000000 --- a/biology/infernal/files/patch-hmmer_src_hmmc2.c +++ /dev/null @@ -1,11 +0,0 @@ ---- 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); diff --git a/biology/infernal/files/patch-src_Makefile.in b/biology/infernal/files/patch-src_Makefile.in deleted file mode 100644 index 7afaa0ab41ea..000000000000 --- a/biology/infernal/files/patch-src_Makefile.in +++ /dev/null @@ -1,19 +0,0 @@ ---- 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}
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