aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorJason W. Bacon <jwb@FreeBSD.org>2022-10-11 18:58:39 +0000
committerJason W. Bacon <jwb@FreeBSD.org>2022-10-11 20:13:01 +0000
commitb532c5dd966eb638a5616fc7819657f007c08848 (patch)
treecddeb3bfbfdc0041d6fdcceea934dd5d220b4799
parent7d9dd3c7672041918cf7e41ace76180ba84b88f0 (diff)
downloadports-b532c5dd966eb638a5616fc7819657f007c08848.tar.gz
ports-b532c5dd966eb638a5616fc7819657f007c08848.zip
biology/hmmer: Update to 3.3.2
No release notes. See commits for changes: https://github.com/EddyRivasLab/hmmer PR: 266968 Reported by: mzaki@e-mail.ne.jp
-rw-r--r--biology/hmmer/Makefile16
-rw-r--r--biology/hmmer/distinfo6
-rw-r--r--biology/hmmer/files/patch-src_hmmc2.c11
3 files changed, 11 insertions, 22 deletions
diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
index 3773440431c7..21a16114e1d5 100644
--- a/biology/hmmer/Makefile
+++ b/biology/hmmer/Makefile
@@ -1,5 +1,5 @@
PORTNAME= hmmer
-PORTVERSION= 3.3
+PORTVERSION= 3.3.2
CATEGORIES= biology
MASTER_SITES= http://eddylab.org/software/hmmer/
@@ -14,14 +14,14 @@ ONLY_FOR_ARCHS= amd64 i386 powerpc powerpc64
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
@@ -30,14 +30,11 @@ EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \
Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.sto \
globins4.hmm globins4.sto globins45.fa
-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/*
@@ -49,4 +46,7 @@ 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/hmmer/distinfo b/biology/hmmer/distinfo
index 4af97cebbada..edb75ddf6465 100644
--- a/biology/hmmer/distinfo
+++ b/biology/hmmer/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1578579116
-SHA256 (hmmer-3.3.tar.gz) = 0186bf40af67032666014971ed8ddc3cf2834bebc2be5b3bc0304a93e763736c
-SIZE (hmmer-3.3.tar.gz) = 18614771
+TIMESTAMP = 1665491511
+SHA256 (hmmer-3.3.2.tar.gz) = 92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69
+SIZE (hmmer-3.3.2.tar.gz) = 18213049
diff --git a/biology/hmmer/files/patch-src_hmmc2.c b/biology/hmmer/files/patch-src_hmmc2.c
deleted file mode 100644
index 8d16156a130c..000000000000
--- a/biology/hmmer/files/patch-src_hmmc2.c
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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);