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biology/hmmer: update to 3.3

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PR:	243244
Submitted by:	mzaki@e-mail.ne.jp (maintainer)
This commit is contained in:
Fernando Apesteguía 2020-01-29 05:55:12 +00:00
parent ef40379829
commit b1a429edf6
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=524533
4 changed files with 26 additions and 9 deletions
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15
biology/hmmer/Makefile
View File

@ -2,12 +2,11 @@
# $FreeBSD$
PORTNAME= hmmer
PORTVERSION= 3.2.1
PORTREVISION= 1
PORTVERSION= 3.3
CATEGORIES= biology
MASTER_SITES= http://eddylab.org/software/hmmer/
MAINTAINER= mzaki@niid.go.jp
MAINTAINER= mzaki@e-mail.ne.jp
COMMENT= Profile hidden Markov models for biological sequence analysis
LICENSE= BSD3CLAUSE
@ -16,14 +15,14 @@ LICENSE_FILE= ${WRKSRC}/LICENSE
ONLY_FOR_ARCHS= amd64 i386 powerpc powerpc64 powerpcspe
ONLY_FOR_ARCHS_REASON= requires SSE2 or AltiVec instructions
USES= compiler:c11 gmake perl5 shebangfix
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
SHEBANG_GLOB= *.pl *.py
SHEBANG_FILES= easel/devkit/*
OPTIONS_DEFINE= DOCS EXAMPLES TEST
@ -34,8 +33,12 @@ EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \
globins4.hmm globins4.sto globins45.fa
TEST_VARS= use_perl5=build
TEST_BUILD_DEPENDS= ${PYTHON_VERSION}:lang/python${PYTHON_SUFFIX}
post-build-TEST-on: do-test
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/*

6
biology/hmmer/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1531293655
SHA256 (hmmer-3.2.1.tar.gz) = a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c
SIZE (hmmer-3.2.1.tar.gz) = 7670274
TIMESTAMP = 1578579116
SHA256 (hmmer-3.3.tar.gz) = 0186bf40af67032666014971ed8ddc3cf2834bebc2be5b3bc0304a93e763736c
SIZE (hmmer-3.3.tar.gz) = 18614771

11
biology/hmmer/files/patch-src_hmmc2.c Normal file
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@ -0,0 +1,11 @@
--- src/hmmc2.c.orig 2019-11-18 13:23:12 UTC
+++ 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);

3
biology/hmmer/pkg-plist
View File

@ -6,6 +6,7 @@ bin/hmmemit
bin/hmmfetch
bin/hmmlogo
bin/hmmpgmd
bin/hmmpgmd_shard
bin/hmmpress
bin/hmmscan
bin/hmmsearch
@ -19,12 +20,14 @@ bin/phmmer
man/man1/alimask.1.gz
man/man1/hmmalign.1.gz
man/man1/hmmbuild.1.gz
man/man1/hmmc2.1.gz
man/man1/hmmconvert.1.gz
man/man1/hmmemit.1.gz
man/man1/hmmer.1.gz
man/man1/hmmfetch.1.gz
man/man1/hmmlogo.1.gz
man/man1/hmmpgmd.1.gz
man/man1/hmmpgmd_shard.1.gz
man/man1/hmmpress.1.gz
man/man1/hmmscan.1.gz
man/man1/hmmsearch.1.gz