diff options
Diffstat (limited to 'biology/infernal')
| -rw-r--r-- | biology/infernal/Makefile | 29 | ||||
| -rw-r--r-- | biology/infernal/distinfo | 6 | ||||
| -rw-r--r-- | biology/infernal/files/patch-configure | 10 | ||||
| -rw-r--r-- | biology/infernal/files/patch-hmmer_src_hmmc2.c | 11 | ||||
| -rw-r--r-- | biology/infernal/files/patch-src_Makefile.in | 19 |
5 files changed, 53 insertions, 22 deletions
diff --git a/biology/infernal/Makefile b/biology/infernal/Makefile index 9e65537af33d..8ecde37b71ac 100644 --- a/biology/infernal/Makefile +++ b/biology/infernal/Makefile @@ -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 \ @@ -27,13 +35,16 @@ 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 -OPTIONS_DEFINE= DOCS EXAMPLES TEST +TEST_VARS= use_perl5=build +TEST_BUILD_DEPENDS= ${PYTHON_VERSION}:lang/python${PYTHON_SUFFIX} + +post-build-TEST-on: pre-test do-test -TEST_TEST_TARGET= check -TEST_USES= shebangfix perl5 -TEST_VARS= shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build +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-build-TEST-on: do-test +post-install: + @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/* post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} diff --git a/biology/infernal/distinfo b/biology/infernal/distinfo index a99bece6070f..9f362448abc8 100644 --- a/biology/infernal/distinfo +++ b/biology/infernal/distinfo @@ -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 diff --git a/biology/infernal/files/patch-configure b/biology/infernal/files/patch-configure deleted file mode 100644 index f9fdfd5f3f0d..000000000000 --- a/biology/infernal/files/patch-configure +++ /dev/null @@ -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;; diff --git a/biology/infernal/files/patch-hmmer_src_hmmc2.c b/biology/infernal/files/patch-hmmer_src_hmmc2.c new file mode 100644 index 000000000000..5bd86cf55247 --- /dev/null +++ b/biology/infernal/files/patch-hmmer_src_hmmc2.c @@ -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); diff --git a/biology/infernal/files/patch-src_Makefile.in b/biology/infernal/files/patch-src_Makefile.in new file mode 100644 index 000000000000..7afaa0ab41ea --- /dev/null +++ b/biology/infernal/files/patch-src_Makefile.in @@ -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} |