Date: Tue, 11 Oct 2022 20:13:02 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: b532c5dd966e - main - biology/hmmer: Update to 3.3.2 Message-ID: <202210112013.29BKD22l074829@gitrepo.freebsd.org>
next in thread | raw e-mail | index | archive | help
The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=b532c5dd966eb638a5616fc7819657f007c08848 commit b532c5dd966eb638a5616fc7819657f007c08848 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2022-10-11 18:58:39 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2022-10-11 20:13:01 +0000 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 --- biology/hmmer/Makefile | 16 ++++++++-------- biology/hmmer/distinfo | 6 +++--- biology/hmmer/files/patch-src_hmmc2.c | 11 ----------- 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);
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202210112013.29BKD22l074829>