From owner-dev-commits-ports-all@freebsd.org Tue Apr 13 00:29:36 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 845305E2F5D; Tue, 13 Apr 2021 00:29:36 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4FK61X3LL7z3Kt3; Tue, 13 Apr 2021 00:29:36 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 6144B2138C; Tue, 13 Apr 2021 00:29:36 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 13D0TaWZ096952; Tue, 13 Apr 2021 00:29:36 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 13D0Ta4Q096951; Tue, 13 Apr 2021 00:29:36 GMT (envelope-from git) Date: Tue, 13 Apr 2021 00:29:36 GMT Message-Id: <202104130029.13D0Ta4Q096951@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: fd20bf82b699 - main - biology/mothur: Update to 1.45.2 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: fd20bf82b699c91e1ddc0b92ddc98b038483c706 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 13 Apr 2021 00:29:36 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=fd20bf82b699c91e1ddc0b92ddc98b038483c706 commit fd20bf82b699c91e1ddc0b92ddc98b038483c706 Author: Jason W. Bacon AuthorDate: 2021-04-13 00:27:03 +0000 Commit: Jason W. Bacon CommitDate: 2021-04-13 00:29:17 +0000 biology/mothur: Update to 1.45.2 Numerous bug fixes and enhancements since 1.43.0 Approved by: yuri --- biology/mothur/Makefile | 5 ++--- biology/mothur/distinfo | 6 +++--- biology/mothur/files/patch-Makefile | 23 +++++++++++++++++++--- .../mothur/files/patch-source_endiannessmacros.h | 19 ------------------ 4 files changed, 25 insertions(+), 28 deletions(-) diff --git a/biology/mothur/Makefile b/biology/mothur/Makefile index cd379b8b9e23..052c7316a429 100644 --- a/biology/mothur/Makefile +++ b/biology/mothur/Makefile @@ -1,6 +1,6 @@ PORTNAME= mothur DISTVERSIONPREFIX= v -DISTVERSION= 1.43.0 +DISTVERSION= 1.45.2 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org @@ -11,8 +11,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE.md BUILD_DEPENDS= bash:shells/bash -USES= compiler:c++11-lang gmake localbase readline shebangfix -SHEBANG_FILES= source/uchime_src/mk +USES= compiler:c++11-lang gmake localbase readline USE_GITHUB= yes ALL_TARGET= ${PORTNAME} diff --git a/biology/mothur/distinfo b/biology/mothur/distinfo index a1cbdc3202d9..aa53703b0440 100644 --- a/biology/mothur/distinfo +++ b/biology/mothur/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1570294640 -SHA256 (mothur-mothur-v1.43.0_GH0.tar.gz) = 12ccd95a85bec3bb1564b8feabd244ea85413973740754803d01fc71ecb0a2c1 -SIZE (mothur-mothur-v1.43.0_GH0.tar.gz) = 1665073 +TIMESTAMP = 1618235513 +SHA256 (mothur-mothur-v1.45.2_GH0.tar.gz) = 73fddddfeea140537b8b037da971964091b2149177e376d98d19ba8a2183e471 +SIZE (mothur-mothur-v1.45.2_GH0.tar.gz) = 1614451 diff --git a/biology/mothur/files/patch-Makefile b/biology/mothur/files/patch-Makefile index 9d0709f1ea26..106b43e4e311 100644 --- a/biology/mothur/files/patch-Makefile +++ b/biology/mothur/files/patch-Makefile @@ -1,6 +1,16 @@ ---- Makefile.orig 2019-09-30 19:02:13 UTC +--- Makefile.orig 2021-04-09 18:28:13 UTC +++ Makefile -@@ -100,7 +100,7 @@ endif +@@ -53,6 +53,9 @@ endif + CXXFLAGS += -std=c++11 -pthread -DVERSION=${VERSION} -DRELEASE_DATE=${RELEASE_DATE} + LDFLAGS += -std=c++11 -pthread + ++# uchime requires gmake ++MAKE ?= gmake ++ + ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"") + else + CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES} +@@ -109,7 +112,7 @@ endif subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/)))) subDirIncludes = $(patsubst %, -I %, $(subdirs)) subDirLinking = $(patsubst %, -L%, $(subdirs)) @@ -9,7 +19,7 @@ LDFLAGS += $(subDirLinking) -@@ -109,8 +109,8 @@ endif +@@ -118,14 +121,14 @@ endif # OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs)))) OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs)))) @@ -20,3 +30,10 @@ mothur : $(OBJECTS) uchime $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) + + uchime : +- cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv uchime ../../ && cd .. ++ cd source/uchime_src && export CXX=$(CXX) && ${MAKE} clean && ${MAKE} && mv uchime ../../ && cd .. + + install : mothur + diff --git a/biology/mothur/files/patch-source_endiannessmacros.h b/biology/mothur/files/patch-source_endiannessmacros.h deleted file mode 100644 index 923cfbd9e621..000000000000 --- a/biology/mothur/files/patch-source_endiannessmacros.h +++ /dev/null @@ -1,19 +0,0 @@ ---- source/endiannessmacros.h.orig 2020-10-19 10:22:23 UTC -+++ source/endiannessmacros.h -@@ -53,16 +53,6 @@ - # define SP_BIG_ENDIAN - #endif - --/* -- * PowerPC -- */ --#if defined(__ppc__) || defined(__ppc) --# if defined(SP_LITTLE_ENDIAN) --# undef SP_LITTLE_ENDIAN --# endif --# define SP_BIG_ENDIAN --#endif -- - /* Some catch-alls */ - #if defined(__LITTLE_ENDIAN__) || defined(__LITTLEENDIAN__) - # define SP_LITTLE_ENDIAN