Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id D9DC784ED3 for ; Wed, 8 Nov 2023 16:46:45 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id qNmwusflDwO6 for ; Wed, 8 Nov 2023 16:46:45 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id 100F984D5E for ; Wed, 8 Nov 2023 16:46:45 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 093ACFA2F; Wed, 8 Nov 2023 16:46:45 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1699462005100710" MIME-Version: 1.0 Date: Wed, 8 Nov 2023 16:46:45 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/bedtools To: pkgsrc-changes@NetBSD.org Approved: commit_and_comment Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20231108164645.093ACFA2F@cvs.NetBSD.org> This is a multi-part message in MIME format. --_----------=_1699462005100710 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Wed Nov 8 16:46:44 UTC 2023 Modified Files: pkgsrc/biology/bedtools: DESCR Makefile distinfo pkgsrc/biology/bedtools/patches: patch-Makefile Log Message: biology/bedtools: Update to 2.31.1 Code updates for modern compilers Changes: https://github.com/arq5x/bedtools2/releases To generate a diff of this commit: cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/bedtools/DESCR cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/bedtools/Makefile cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/bedtools/distinfo cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/bedtools/patches/patch-Makefile Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1699462005100710 Content-Disposition: inline Content-Length: 5767 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/bedtools/DESCR diff -u pkgsrc/biology/bedtools/DESCR:1.1 pkgsrc/biology/bedtools/DESCR:1.2 --- pkgsrc/biology/bedtools/DESCR:1.1 Fri Jan 22 17:07:50 2021 +++ pkgsrc/biology/bedtools/DESCR Wed Nov 8 16:46:44 2023 @@ -1,10 +1,11 @@ -The bedtools utilities are a suite of tools for performing a wide range of -genomics analysis tasks. The most widely-used of these tools enable genome -arithmetic, i.e., set theory on the genome. For example, with bedtools one -can intersect, merge, count, complement, and shuffle genomic intervals from -multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF. +The bedtools utilities are a suite of tools for performing a wide +range of genomics analysis tasks. The most widely-used of these +tools enable genome arithmetic, i.e., set theory on the genome. +For example, with bedtools one can intersect, merge, count, +complement, and shuffle genomic intervals from multiple files in +common genomic formats such as BAM, BED, GFF/GTF, and VCF. -Although each individual utility is designed to do a relatively simple task, -e.g., intersect two interval files, more sophisticated analyses can be -conducted by stringing together multiple bedtools operations on the command -line or in shell scripts. +Although each individual utility is designed to do a relatively +simple task, e.g., intersect two interval files, more sophisticated +analyses can be conducted by stringing together multiple bedtools +operations on the command line or in shell scripts. Index: pkgsrc/biology/bedtools/Makefile diff -u pkgsrc/biology/bedtools/Makefile:1.5 pkgsrc/biology/bedtools/Makefile:1.6 --- pkgsrc/biology/bedtools/Makefile:1.5 Mon Aug 14 05:23:51 2023 +++ pkgsrc/biology/bedtools/Makefile Wed Nov 8 16:46:44 2023 @@ -1,13 +1,12 @@ -# $NetBSD: Makefile,v 1.5 2023/08/14 05:23:51 wiz Exp $ +# $NetBSD: Makefile,v 1.6 2023/11/08 16:46:44 bacon Exp $ -DISTNAME= bedtools-2.30.0 -PKGREVISION= 2 +DISTNAME= bedtools-2.31.1 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=arq5x/} GITHUB_PROJECT= bedtools2 GITHUB_TAG= v${PKGVERSION_NOREV} -MAINTAINER= bacon@NetBSD.org +OWNER= bacon@NetBSD.org HOMEPAGE= https://bedtools.readthedocs.io/en/latest/ COMMENT= Swiss army knife for genome arithmetic LICENSE= mit @@ -17,13 +16,13 @@ USE_TOOLS+= bash:test gmake REPLACE_SH+= scripts/vcfsort.sh REPLACE_PYTHON= scripts/makeBashScripts.py -LDFLAGS.SunOS+= -lsocket - SUBST_CLASSES+= pybin SUBST_STAGE.pybin= pre-configure SUBST_SED.pybin= -e 's|python|${PYTHONBIN}|g' SUBST_FILES.pybin= Makefile +LDFLAGS.SunOS+= -lsocket + do-test: cd ${WRKSRC}/test && bash test.sh Index: pkgsrc/biology/bedtools/distinfo diff -u pkgsrc/biology/bedtools/distinfo:1.4 pkgsrc/biology/bedtools/distinfo:1.5 --- pkgsrc/biology/bedtools/distinfo:1.4 Tue Oct 26 10:03:37 2021 +++ pkgsrc/biology/bedtools/distinfo Wed Nov 8 16:46:44 2023 @@ -1,9 +1,9 @@ -$NetBSD: distinfo,v 1.4 2021/10/26 10:03:37 nia Exp $ +$NetBSD: distinfo,v 1.5 2023/11/08 16:46:44 bacon Exp $ -BLAKE2s (bedtools-2.30.0.tar.gz) = f4e0cdb0d7ca32da2724c1afcf707c02a02ab201b66b93e4ce26d9a51e0566c5 -SHA512 (bedtools-2.30.0.tar.gz) = 3d69d6a53d3e5d15597dfefa26f7895231adbf3c1fe3b16ee4213e497ef01a20698add2f0e6f03d8eb7cd7c70709955f0ebdf897a025a83d31ef17e2c91f9856 -Size (bedtools-2.30.0.tar.gz) = 20639858 bytes -SHA1 (patch-Makefile) = d21b4a69ce18eac7de59d277a03d0a5f5e2e1cb5 +BLAKE2s (bedtools-2.31.1.tar.gz) = e5b3faf919f7aaf12251b29fa248e85248ec30dadab45c3fd23523d7ddc78c05 +SHA512 (bedtools-2.31.1.tar.gz) = b62feeb6ef211314a86e022b6104cc2291086b940913cff5878759c37a8be0ac50c174020d8555d71dbc29e6be56ea40fc3c6543b5ef444bc7535124814688d6 +Size (bedtools-2.31.1.tar.gz) = 21085970 bytes +SHA1 (patch-Makefile) = f38634cad79026c0dd0cad6a6a70db933f002d5f SHA1 (patch-src_utils_BamTools_include_SamHeader.hpp) = 7ab168b247b5edf7f3eccd9ef7329a5e1605c787 SHA1 (patch-src_utils_htslib_Makefile) = 8785ff3110f8df26e0cc5b2fdf1e2e02d6cdc836 SHA1 (patch-test_test.sh) = e3a17815d6a30c17db7134613d25f08c6be3494e Index: pkgsrc/biology/bedtools/patches/patch-Makefile diff -u pkgsrc/biology/bedtools/patches/patch-Makefile:1.2 pkgsrc/biology/bedtools/patches/patch-Makefile:1.3 --- pkgsrc/biology/bedtools/patches/patch-Makefile:1.2 Mon Feb 8 01:49:25 2021 +++ pkgsrc/biology/bedtools/patches/patch-Makefile Wed Nov 8 16:46:44 2023 @@ -1,8 +1,8 @@ -$NetBSD: patch-Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $ +$NetBSD: patch-Makefile,v 1.3 2023/11/08 16:46:44 bacon Exp $ -# Respect pkgsrc env, drop bash dep +# Portability, respect env ---- Makefile.orig 2021-02-05 21:42:03.926301547 +0000 +--- Makefile.orig 2023-11-08 15:05:30.454330622 +0000 +++ Makefile @@ -4,7 +4,7 @@ # (c) 2009 Aaron Quinlan @@ -20,9 +20,9 @@ $NetBSD: patch-Makefile,v 1.2 2021/02/08 -CXX = g++ +CXX ?= g++ - ifeq ($(DEBUG),1) - BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES) -@@ -41,7 +41,7 @@ endif + PYTHON ?= $(shell python --version >/dev/null 2>&1 && echo "python" || echo python3) + +@@ -43,7 +43,7 @@ endif BT_LDFLAGS = BT_LIBS = -lz -lm -lbz2 -llzma -lpthread @@ -31,16 +31,16 @@ $NetBSD: patch-Makefile,v 1.2 2021/02/08 SUBDIRS = $(SRC_DIR)/annotateBed \ $(SRC_DIR)/bamToBed \ -@@ -155,7 +155,7 @@ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_C +@@ -158,7 +158,7 @@ $(CCPREFIX) $(CC_WRAPPER) $(CXX) $(ALL_C @mv -f $*.Td $*.d endef -$(OBJ_DIR)/%.d: ; -+$(OBJ_DIR)/%.d: $(OBJ_DIR) ; ++$(OBJ_DIR)/%.d: $(OBJ_DIR); .PRECIOUS: $(OBJ_DIR)/%.d -include $(patsubst %.o,%.d,$(BUILT_OBJECTS)) -@@ -197,9 +197,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR) +@@ -200,9 +200,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR) .PHONY: all install: all --_----------=_1699462005100710--