CVS commit: pkgsrc/biology/bedtools

["Jason Bacon" <bacon%netbsd.org@localhost>]

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.

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@localhost
+OWNER=         bacon%NetBSD.org@localhost
 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