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| author | Fernando Apesteguía <fernape@FreeBSD.org> | 2020-01-29 05:55:12 +0000 |
|---|---|---|
| committer | Fernando Apesteguía <fernape@FreeBSD.org> | 2020-01-29 05:55:12 +0000 |
| commit | b1a429edf61c6d4e0bc3d74eb8cc5b35d8e34312 (patch) | |
| tree | 2017b49090f47556250139cf067d72f2ac202aa2 /biology/hmmer | |
| parent | ef40379829cd916887a1d7012d5df4a73e1e28cc (diff) | |
| download | ports-b1a429edf61c6d4e0bc3d74eb8cc5b35d8e34312.tar.gz ports-b1a429edf61c6d4e0bc3d74eb8cc5b35d8e34312.zip | |
biology/hmmer: update to 3.3
PR: 243244
Submitted by: mzaki@e-mail.ne.jp (maintainer)
Notes
Notes:
svn path=/head/; revision=524533
Diffstat (limited to 'biology/hmmer')
| -rw-r--r-- | biology/hmmer/Makefile | 15 | ||||
| -rw-r--r-- | biology/hmmer/distinfo | 6 | ||||
| -rw-r--r-- | biology/hmmer/files/patch-src_hmmc2.c | 11 | ||||
| -rw-r--r-- | biology/hmmer/pkg-plist | 3 |
4 files changed, 26 insertions, 9 deletions
diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile index 0a4880bc7c95..466d98687eef 100644 --- a/biology/hmmer/Makefile +++ b/biology/hmmer/Makefile @@ -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/* diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo index 5e1694a34b74..4af97cebbada 100644 --- a/biology/hmmer/distinfo +++ b/biology/hmmer/distinfo @@ -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 diff --git a/biology/hmmer/files/patch-src_hmmc2.c b/biology/hmmer/files/patch-src_hmmc2.c new file mode 100644 index 000000000000..8d16156a130c --- /dev/null +++ b/biology/hmmer/files/patch-src_hmmc2.c @@ -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); diff --git a/biology/hmmer/pkg-plist b/biology/hmmer/pkg-plist index e3d8a98cc2d3..03cffa252089 100644 --- a/biology/hmmer/pkg-plist +++ b/biology/hmmer/pkg-plist @@ -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 |