From nobody Sun Jan 19 12:50:09 2025 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4YbYGT3bZ9z5lCYp; Sun, 19 Jan 2025 12:50:09 +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 "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4YbYGT2yY0z3NHv; Sun, 19 Jan 2025 12:50:09 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1737291009; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=5GEhYKysh5HZW8fr8AOtnwbOSBfD2zMM6/P7MqU2q0s=; b=kAhymk7PXB88c9BQX6pxpkbo2FjInk5T0IrBmn8QmD4BeJmq7BlisqOslyGbE9ITpnnw1g eRaYiWJL49xCDS5dYy3r4/RmDgLuz8wogwHwzvPn1SoNGZf48J0CFqNt0agsGdtHs52KwA E1BZA6daJ5YEh6Oa+HarnMrcruQI2bH0N1A8hrG2oJkcGoh/m7ghEMkX9rYMOYHd57ISs1 LbYrWnsI8lqWnQubvk6GMqj/WKot3PLfh0lf8CHFdbgDKXQdQjQSpT+3w8mPvUI+Sjv/xU aGu09chfK9c35b+xL4m9win44moTwNYMm92wC99VhuTk83RApsliVjLYkF2IQg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1737291009; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=5GEhYKysh5HZW8fr8AOtnwbOSBfD2zMM6/P7MqU2q0s=; b=EOedjJA0gF415EqJomXVHHYM1KV87AUDBQlmodFr4Lfp5kzZ4LrDtwD0gS7Ig7cKkWizCM Yqxg7dxLeckAGTWBfNsqqu56oqHHDJnRuVAlp9c3EMKN/Ai6eAjHaWkeO5GVhEObBfAaG2 60AnHJDLhXPj5IV0H3T71OM8s0xj/SN0iInzJFi7lBnxazRdPdpmoWH19kFWKyK/I1X1xh BYKe9xMs2/i+bD6rI2XVq1W4ECDM9gGYF/ws1EXYB4TVorPy9k36SQntBcB4czRpRKDgJ6 gIY3Y/bEAQxBo6VnVKPBLcsvNuSGdOzfrszwQzf6qCNJZ7nqkym5GiC0Z0UUPg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1737291009; a=rsa-sha256; cv=none; b=gYBF5geipXAXj0HBJc45MUB5RWZZfHv7jL1jqMOZJQLQjByKAbAsfsQ/aI/NeAVoRFTKr/ uSUqtK118x1i657vG7W+SfFMxBkmFIOywYVgRWvVpkKn5ov4FFHC3LPAuh6iQ0U5KX6/u9 0MQbYTDVLHsCDfyaG2UBLX9hST3Ex4HHvx9dEiw/E5RRauCUSV+aMPg4VBOTf3huHziQt6 LBsXVynotwkfkmte1uh5oBYQNdhWHCOk4QogF+VCInwAo8uNCcsbnBVGrqMNnIssqhDqiC Djl57IwomGs4uJdmX+CmUVvpJMSoY/Xyo+Lx3bGYW316gz3H8MIKuIVe4+xZvg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none 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 4YbYGT2LLczqd9; Sun, 19 Jan 2025 12:50:09 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 50JCo9mL017629; Sun, 19 Jan 2025 12:50:09 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 50JCo9nR017617; Sun, 19 Jan 2025 12:50:09 GMT (envelope-from git) Date: Sun, 19 Jan 2025 12:50:09 GMT Message-Id: <202501191250.50JCo9nR017617@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: cad392241a59 - main - biology/subread: Update to 2.0.8 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org 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: cad392241a596be06c9caeb29a8f66c194180b95 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=cad392241a596be06c9caeb29a8f66c194180b95 commit cad392241a596be06c9caeb29a8f66c194180b95 Author: Jason W. Bacon AuthorDate: 2025-01-19 12:46:51 +0000 Commit: Jason W. Bacon CommitDate: 2025-01-19 12:46:51 +0000 biology/subread: Update to 2.0.8 A few fixes and updates since 2.0.2 Changes: https://subread.sourceforge.net/ PR: 283261 Reported by: alster@vinterdalen.se --- biology/subread/Makefile | 10 ++++++---- biology/subread/distinfo | 6 +++--- biology/subread/files/patch-longread-one_Makefile | 16 +++++++++------- 3 files changed, 18 insertions(+), 14 deletions(-) diff --git a/biology/subread/Makefile b/biology/subread/Makefile index f1d4b49106e1..e94ede742f9a 100644 --- a/biology/subread/Makefile +++ b/biology/subread/Makefile @@ -1,12 +1,12 @@ PORTNAME= subread -DISTVERSION= 2.0.2 +DISTVERSION= 2.0.8 DISTVERSIONSUFFIX= -source CATEGORIES= biology MASTER_SITES= SF/${PORTNAME}/${PORTNAME}-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= High-performance read alignment, quantification and mutation discovery -WWW= http://bioinf.wehi.edu.au/subread-package/ +WWW= https://subread.sourceforge.net/ LICENSE= GPLv3 LICENSE_FILE= ${WRKDIR}/${DISTNAME}/LICENSE @@ -15,9 +15,11 @@ LIB_DEPENDS= libsysinfo.so:devel/libsysinfo USES= gmake localbase:ldflags -MAKEFILE= ${FILESDIR}/Makefile.pkg WRKSRC_SUBDIR= src -CFLAGS+= -fcommon + +MAKEFILE= ${FILESDIR}/Makefile.pkg INSTALL_TARGET= install-strip +CFLAGS+= -fcommon + .include diff --git a/biology/subread/distinfo b/biology/subread/distinfo index 65c193e7ae1a..7e6e9e5f7d23 100644 --- a/biology/subread/distinfo +++ b/biology/subread/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1617112862 -SHA256 (subread-2.0.2-source.tar.gz) = 0b64bd51f39f8d322c4594697fa5f0f64fbe60283113eadadff9f4268f897079 -SIZE (subread-2.0.2-source.tar.gz) = 23295764 +TIMESTAMP = 1733935409 +SHA256 (subread-2.0.8-source.tar.gz) = cb5dadf71c850f128a8347223fe0ce19e1c17e3959e9f3eba90e8090671f8570 +SIZE (subread-2.0.8-source.tar.gz) = 26074498 diff --git a/biology/subread/files/patch-longread-one_Makefile b/biology/subread/files/patch-longread-one_Makefile index ef09f35cd441..41a2a468ea37 100644 --- a/biology/subread/files/patch-longread-one_Makefile +++ b/biology/subread/files/patch-longread-one_Makefile @@ -1,4 +1,4 @@ ---- longread-one/Makefile.orig 2019-09-04 04:22:49 UTC +--- longread-one/Makefile.orig 2024-07-25 00:35:55 UTC +++ longread-one/Makefile @@ -1,12 +1,12 @@ -CC_EXEC = gcc @@ -7,24 +7,26 @@ include ../makefile.version include make.version --CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} +-CCFLAGS = ${MACOS} -O${OPT_LEVEL} -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} -LDFLAGS = -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST -CC = ${CC_EXEC} ${CCFLAGS} -fmessage-length=0 -ggdb +CC ?= gcc -+CFLAGS += -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 \ -+ -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} ++CCFLAGS += -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 \ ++ -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} +LDFLAGS += -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS}) -@@ -20,8 +20,8 @@ clean: +@@ -19,9 +19,8 @@ clean: + clean: rm -f *.o LRM - LRM: longread-mapping.c ${ALL_OBJECTS} +-LRM: longread-mapping.c ${ALL_OBJECTS} - ${CC} -o LRM longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS} ++LRM: longread-mapping.c ${ALL_OBJECTS} + ${CC} -o LRM ${CFLAGS} longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS} $(ALL_OBJECTS): $(ALL_C) $(ALL_H) - $(CC) -o $@ -c $(subst .o,.c,$@) +- + $(CC) -o $@ -c ${CFLAGS} $(subst .o,.c,$@) -