* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/
@ 2016-09-24 22:55 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2016-09-24 22:55 UTC (permalink / raw
To: gentoo-commits
commit: c8c95dc5616fe51e1fffe9f875556a5ff14be39e
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 24 22:47:39 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 24 22:55:37 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c8c95dc5
sci-biology/bedtools: Version bump to 2.26.0
Gentoo-bug: 594994
* EAPI=6
* Make buildsystem output verbose
* Inherit 'python-any-r1', due to python script
* Add dependencies for test suite
* Properly set CXX and CXXFLAGS
Package-Manager: portage-2.3.1
sci-biology/bedtools/Manifest | 1 +
sci-biology/bedtools/bedtools-2.26.0.ebuild | 42 +
.../files/bedtools-2.26.0-fix-buildsystem.patch | 869 +++++++++++++++++++++
3 files changed, 912 insertions(+)
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 9dd006e..c5daa59 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,2 +1,3 @@
DIST BEDTools.v2.16.2.tar.gz 978293 SHA256 f5f5c864eb3f465ac7fd5fa651e2e4dbc0cd8d9198367148c52f3be3f46c2772 SHA512 4dfeb048a7eacb1ca70caed64087d279aa955f30cf685f938e5a02ba328d1a878a75bfe37b537fc06cf9023474e4922719f1b391943ff0143c7760e987fa4645 WHIRLPOOL d6b89fdd4dc1f7bebcda71ea7b4c76c5d5811d7b23861019e19667171572743bd8dfbd74d4e80838aa4bfa06a524bcfaf5e76cd52c49b0658929b0060ee3aaa0
DIST bedtools-2.20.1.tar.gz 4213348 SHA256 b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 SHA512 b5c27601365a2126c58492791a52a262c874073cc1626bb1e38545ccf6e3594d12d2d2116304374b3446a588611cfd410c8ff166170823071b33c444c9fd36a7 WHIRLPOOL b768a7e064444d5d0434aea5251e132d68fbeb580783034c8e327666eaace0307febc80e9d6d3eea2f0f648263ce0ac836fac7a676586a6e6a8ec4daf39e6a84
+DIST bedtools-2.26.0.tar.gz 19939711 SHA256 65f32f32cbf1b91ba42854b40c604aa6a16c7d3b3ec110d6acf438eb22df0a4a SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def WHIRLPOOL 8d6e3b58dc38d7ab91482ffe5ee773953864ca79bdbf005b17fec51952a869b39bf775d836ed34496a7784565bb84380eef284e285e842d52229fe2fc6a214b2
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
new file mode 100644
index 00000000..feddd87
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_4,3_5} )
+
+inherit flag-o-matic python-any-r1 toolchain-funcs
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
+HOMEPAGE="https://bedtools.readthedocs.io/"
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="test"
+
+DEPEND="${PYTHON_DEPS}
+ test? (
+ sci-libs/htslib
+ sci-biology/samtools
+ )"
+
+S="${WORKDIR}/${PN}2"
+
+DOCS=( README.md RELEASE_HISTORY )
+PATCHES=( "${FILESDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
+
+src_configure() {
+ append-lfs-flags
+ export prefix="${EPREFIX}/usr"
+ tc-export AR CXX
+}
+
+src_install() {
+ default
+
+ insinto /usr/share/${PN}
+ doins -r genomes
+}
diff --git a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch
new file mode 100644
index 00000000..fb6be18
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch
@@ -0,0 +1,869 @@
+* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308)
+* Remove CXX and CXXFLAGS, ebuild sets them
+* Handle python via Gentoo's EPYTHON instead
+
+--- a/Makefile
++++ b/Makefile
+@@ -16,17 +16,9 @@
+ export BIN_DIR = bin
+ export SRC_DIR = src
+ export UTIL_DIR = src/utils
+-export CXX = g++
+-ifeq ($(DEBUG),1)
+-export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
+-else
+-export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+-endif
+ export LIBS = -lz
+ export BT_ROOT = src/utils/BamTools/
+
+-prefix ?= /usr/local
+-
+ SUBDIRS = $(SRC_DIR)/annotateBed \
+ $(SRC_DIR)/bamToBed \
+ $(SRC_DIR)/bamToFastq \
+@@ -135,13 +127,13 @@
+
+ all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
+ @echo "- Building main bedtools binary."
+- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
+- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
++ $(CXX) $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS)
+ @echo "done."
+
+ @echo "- Creating executables for old CLI."
+- @python scripts/makeBashScripts.py
+- @chmod +x bin/*
++ $(EPYTHON) scripts/makeBashScripts.py
++ chmod +x bin/*
+ @echo "done."
+
+
+--- a/src/annotateBed/Makefile
++++ b/src/annotateBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+
+ clean:
+--- a/src/bamToBed/Makefile
++++ b/src/bamToBed/Makefile
+@@ -28,7 +28,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/bamToFastq/Makefile
++++ b/src/bamToFastq/Makefile
+@@ -24,7 +24,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/bed12ToBed6/Makefile
++++ b/src/bed12ToBed6/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/bedpeToBam/Makefile
++++ b/src/bedpeToBam/Makefile
+@@ -33,7 +33,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
+--- a/src/bedToBam/Makefile
++++ b/src/bedToBam/Makefile
+@@ -30,7 +30,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/bedToIgv/Makefile
++++ b/src/bedToIgv/Makefile
+@@ -28,7 +28,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/closestFile/Makefile
++++ b/src/closestFile/Makefile
+@@ -40,7 +40,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/clusterBed/Makefile
++++ b/src/clusterBed/Makefile
+@@ -25,7 +25,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/complementFile/Makefile
++++ b/src/complementFile/Makefile
+@@ -42,7 +42,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/coverageFile/Makefile
++++ b/src/coverageFile/Makefile
+@@ -38,7 +38,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/expand/Makefile
++++ b/src/expand/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/fastaFromBed/Makefile
++++ b/src/fastaFromBed/Makefile
+@@ -30,7 +30,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/fisher/Makefile
++++ b/src/fisher/Makefile
+@@ -51,7 +51,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/flankBed/Makefile
++++ b/src/flankBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/genomeCoverageBed/Makefile
++++ b/src/genomeCoverageBed/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/getOverlap/Makefile
++++ b/src/getOverlap/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+
+ clean:
+--- a/src/groupBy/Makefile
++++ b/src/groupBy/Makefile
+@@ -42,7 +42,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/intersectFile/Makefile
++++ b/src/intersectFile/Makefile
+@@ -39,7 +39,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/jaccard/Makefile
++++ b/src/jaccard/Makefile
+@@ -43,7 +43,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/linksBed/Makefile
++++ b/src/linksBed/Makefile
+@@ -25,7 +25,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/mapFile/Makefile
++++ b/src/mapFile/Makefile
+@@ -38,7 +38,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/maskFastaFromBed/Makefile
++++ b/src/maskFastaFromBed/Makefile
+@@ -25,7 +25,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/mergeFile/Makefile
++++ b/src/mergeFile/Makefile
+@@ -40,7 +40,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/multiBamCov/Makefile
++++ b/src/multiBamCov/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/multiIntersectBed/Makefile
++++ b/src/multiIntersectBed/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/nekSandbox1/Makefile
++++ b/src/nekSandbox1/Makefile
+@@ -35,7 +35,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/nucBed/Makefile
++++ b/src/nucBed/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/pairToBed/Makefile
++++ b/src/pairToBed/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/pairToPair/Makefile
++++ b/src/pairToPair/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+
+ clean:
+--- a/src/randomBed/Makefile
++++ b/src/randomBed/Makefile
+@@ -23,7 +23,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/regressTest/Makefile
++++ b/src/regressTest/Makefile
+@@ -24,24 +24,18 @@
+ # ----------------------------------
+ # define our source and object files
+ # ----------------------------------
+-#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
+-#OBJECTS= regressTestMain.o RegressTest.o
+-#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
++SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
++OBJECTS= regressTestMain.o RegressTest.o
++BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+ PROGRAM= regressTest
+
+-
+-all: #$(BUILT_OBJECTS)
+- @echo "compiling RegressTest.cpp"
+- @$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+- @echo "compiling regressTestMain.cpp"
+- @$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++all: $(BUILT_OBJECTS)
+
+ .PHONY: all
+
+-#$(BUILT_OBJECTS): $(SOURCES)
+-# @echo " * compiling" $(*F).cpp
+-# @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
+-
++$(BUILT_OBJECTS): $(SOURCES)
++ @echo " * compiling" $(*F).cpp
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/reldist/Makefile
++++ b/src/reldist/Makefile
+@@ -30,7 +30,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/sampleFile/Makefile
++++ b/src/sampleFile/Makefile
+@@ -37,7 +37,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/shiftBed/Makefile
++++ b/src/shiftBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/shuffleBed/Makefile
++++ b/src/shuffleBed/Makefile
+@@ -28,7 +28,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/slopBed/Makefile
++++ b/src/slopBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/sortBed/Makefile
++++ b/src/sortBed/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/spacingFile/Makefile
++++ b/src/spacingFile/Makefile
+@@ -37,7 +37,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/split/Makefile
++++ b/src/split/Makefile
+@@ -25,7 +25,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/subtractFile/Makefile
++++ b/src/subtractFile/Makefile
+@@ -40,7 +40,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/tagBam/Makefile
++++ b/src/tagBam/Makefile
+@@ -28,7 +28,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/unionBedGraphs/Makefile
++++ b/src/unionBedGraphs/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/BamTools/Makefile
++++ b/src/utils/BamTools/Makefile
+@@ -56,12 +56,12 @@
+
+ $(LIBRARY): $(OBJECTS)
+ @echo " * linking $(LIBRARY)"
+- ar cr $@ $^
++ $(AR) cr $@ $^
+ -ranlib $@
+
+ $(OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o -c $(*D)/$(*F).cpp
+
+ .PHONY: api
+ api:
+--- a/src/utils/BamTools-Ancillary/Makefile
++++ b/src/utils/BamTools-Ancillary/Makefile
+@@ -21,7 +21,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/bedFile/Makefile
++++ b/src/utils/bedFile/Makefile
+@@ -20,7 +20,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C -W $(INCLUDES)
+--- a/src/utils/bedFilePE/Makefile
++++ b/src/utils/bedFilePE/Makefile
+@@ -17,7 +17,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- a/src/utils/bedGraphFile/Makefile
++++ b/src/utils/bedGraphFile/Makefile
+@@ -19,7 +19,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C -W $(INCLUDES)
+--- a/src/utils/BinTree/Makefile
++++ b/src/utils/BinTree/Makefile
+@@ -28,7 +28,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- a/src/utils/BlockedIntervals/Makefile
++++ b/src/utils/BlockedIntervals/Makefile
+@@ -23,7 +23,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- a/src/utils/chromsweep/Makefile
++++ b/src/utils/chromsweep/Makefile
+@@ -20,7 +20,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- a/src/utils/Contexts/Makefile
++++ b/src/utils/Contexts/Makefile
+@@ -36,7 +36,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/driver/Makefile
++++ b/src/utils/driver/Makefile
+@@ -85,7 +85,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/Fasta/Makefile
++++ b/src/utils/Fasta/Makefile
+@@ -19,7 +19,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/FileRecordTools/FileReaders/Makefile
++++ b/src/utils/FileRecordTools/FileReaders/Makefile
+@@ -32,7 +32,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/FileRecordTools/FileReaders/Makefile~
++++ b/src/utils/FileRecordTools/FileReaders/Makefile~
+@@ -31,7 +31,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/FileRecordTools/Makefile
++++ b/src/utils/FileRecordTools/Makefile
+@@ -34,9 +34,9 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling FileRecordMgr.cpp"
+- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp
+ @echo " * compiling FileRecordMergeMgr.cpp"
+- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp
+
+
+
+--- a/src/utils/FileRecordTools/Records/Makefile
++++ b/src/utils/FileRecordTools/Records/Makefile
+@@ -37,7 +37,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/fileType/Makefile
++++ b/src/utils/fileType/Makefile
+@@ -22,7 +22,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/general/Makefile
++++ b/src/utils/general/Makefile
+@@ -21,7 +21,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/GenomeFile/Makefile
++++ b/src/utils/GenomeFile/Makefile
+@@ -20,9 +20,9 @@
+
+ $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
+ @echo " * compiling GenomeFile.cpp"
+- @$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp
+ @echo " * compiling NewGenomeFile.cpp"
+- @$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp
+
+ #$(EXT_OBJECTS):
+ # @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
+--- a/src/utils/gzstream/Makefile
++++ b/src/utils/gzstream/Makefile
+@@ -38,7 +38,7 @@
+ UTILITIES_DIR = ../../utils/
+
+ ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h
+- $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/gzstream.o gzstream.C
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/KeyListOps/Makefile
++++ b/src/utils/KeyListOps/Makefile
+@@ -31,7 +31,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+
+ $(EXT_OBJECTS):
+--- a/src/utils/NewChromsweep/Makefile
++++ b/src/utils/NewChromsweep/Makefile
+@@ -34,7 +34,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/RecordOutputMgr/Makefile
++++ b/src/utils/RecordOutputMgr/Makefile
+@@ -29,7 +29,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- a/src/utils/sequenceUtilities/Makefile
++++ b/src/utils/sequenceUtilities/Makefile
+@@ -17,7 +17,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- a/src/utils/tabFile/Makefile
++++ b/src/utils/tabFile/Makefile
+@@ -19,7 +19,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C -W $(INCLUDES)
+--- a/src/utils/ToolBase/Makefile
++++ b/src/utils/ToolBase/Makefile
+@@ -30,7 +30,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+--- a/src/utils/VectorOps/Makefile
++++ b/src/utils/VectorOps/Makefile
+@@ -11,7 +11,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/utils/version/Makefile
++++ b/src/utils/version/Makefile
+@@ -20,7 +20,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES) $(HEADERS)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/windowBed/Makefile
++++ b/src/windowBed/Makefile
+@@ -27,7 +27,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ clean:
+ @echo "Cleaning up."
+--- a/src/windowMaker/Makefile
++++ b/src/windowMaker/Makefile
+@@ -26,7 +26,7 @@
+
+ $(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
+
+ $(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/
@ 2017-12-10 0:05 Michał Górny
0 siblings, 0 replies; 6+ messages in thread
From: Michał Górny @ 2017-12-10 0:05 UTC (permalink / raw
To: gentoo-commits
commit: 96adca668f64cdeb561fab922e1489e8f5aa01de
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sat Dec 9 23:15:36 2017 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Dec 10 00:05:27 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=96adca66
sci-biology/bedtools: [QA] Move patch to a distfile
Closes: https://bugs.gentoo.org/620612
sci-biology/bedtools/Manifest | 3 +-
sci-biology/bedtools/bedtools-2.26.0.ebuild | 7 +-
.../files/bedtools-2.26.0-fix-buildsystem.patch | 869 ---------------------
3 files changed, 6 insertions(+), 873 deletions(-)
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index e398b3bee6f..642fe852658 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1 +1,2 @@
-DIST bedtools-2.26.0.tar.gz 19939711 SHA256 65f32f32cbf1b91ba42854b40c604aa6a16c7d3b3ec110d6acf438eb22df0a4a SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def WHIRLPOOL 8d6e3b58dc38d7ab91482ffe5ee773953864ca79bdbf005b17fec51952a869b39bf775d836ed34496a7784565bb84380eef284e285e842d52229fe2fc6a214b2
+DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3
+DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index eeedf606deb..0520143f3d9 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -9,7 +9,8 @@ inherit flag-o-matic python-any-r1 toolchain-funcs
DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
HOMEPAGE="https://bedtools.readthedocs.io/"
-SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz
+ https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2"
LICENSE="GPL-2"
SLOT="0"
@@ -26,7 +27,7 @@ RDEPEND="sys-libs/zlib"
S="${WORKDIR}/${PN}2"
DOCS=( README.md RELEASE_HISTORY )
-PATCHES=( "${FILESDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
+PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" )
src_configure() {
append-lfs-flags
diff --git a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch
deleted file mode 100644
index fb6be18d707..00000000000
--- a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch
+++ /dev/null
@@ -1,869 +0,0 @@
-* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308)
-* Remove CXX and CXXFLAGS, ebuild sets them
-* Handle python via Gentoo's EPYTHON instead
-
---- a/Makefile
-+++ b/Makefile
-@@ -16,17 +16,9 @@
- export BIN_DIR = bin
- export SRC_DIR = src
- export UTIL_DIR = src/utils
--export CXX = g++
--ifeq ($(DEBUG),1)
--export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
--else
--export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
--endif
- export LIBS = -lz
- export BT_ROOT = src/utils/BamTools/
-
--prefix ?= /usr/local
--
- SUBDIRS = $(SRC_DIR)/annotateBed \
- $(SRC_DIR)/bamToBed \
- $(SRC_DIR)/bamToFastq \
-@@ -135,13 +127,13 @@
-
- all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
- @echo "- Building main bedtools binary."
-- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
-- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
-+ $(CXX) $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS)
- @echo "done."
-
- @echo "- Creating executables for old CLI."
-- @python scripts/makeBashScripts.py
-- @chmod +x bin/*
-+ $(EPYTHON) scripts/makeBashScripts.py
-+ chmod +x bin/*
- @echo "done."
-
-
---- a/src/annotateBed/Makefile
-+++ b/src/annotateBed/Makefile
-@@ -26,7 +26,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
-
- clean:
---- a/src/bamToBed/Makefile
-+++ b/src/bamToBed/Makefile
-@@ -28,7 +28,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/bamToFastq/Makefile
-+++ b/src/bamToFastq/Makefile
-@@ -24,7 +24,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/bed12ToBed6/Makefile
-+++ b/src/bed12ToBed6/Makefile
-@@ -27,7 +27,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/bedpeToBam/Makefile
-+++ b/src/bedpeToBam/Makefile
-@@ -33,7 +33,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/
---- a/src/bedToBam/Makefile
-+++ b/src/bedToBam/Makefile
-@@ -30,7 +30,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/bedToIgv/Makefile
-+++ b/src/bedToIgv/Makefile
-@@ -28,7 +28,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/closestFile/Makefile
-+++ b/src/closestFile/Makefile
-@@ -40,7 +40,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/clusterBed/Makefile
-+++ b/src/clusterBed/Makefile
-@@ -25,7 +25,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/complementFile/Makefile
-+++ b/src/complementFile/Makefile
-@@ -42,7 +42,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/coverageFile/Makefile
-+++ b/src/coverageFile/Makefile
-@@ -38,7 +38,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/expand/Makefile
-+++ b/src/expand/Makefile
-@@ -27,7 +27,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/fastaFromBed/Makefile
-+++ b/src/fastaFromBed/Makefile
-@@ -30,7 +30,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/fisher/Makefile
-+++ b/src/fisher/Makefile
-@@ -51,7 +51,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/flankBed/Makefile
-+++ b/src/flankBed/Makefile
-@@ -26,7 +26,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/genomeCoverageBed/Makefile
-+++ b/src/genomeCoverageBed/Makefile
-@@ -27,7 +27,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/getOverlap/Makefile
-+++ b/src/getOverlap/Makefile
-@@ -26,7 +26,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
-
- clean:
---- a/src/groupBy/Makefile
-+++ b/src/groupBy/Makefile
-@@ -42,7 +42,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/intersectFile/Makefile
-+++ b/src/intersectFile/Makefile
-@@ -39,7 +39,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/jaccard/Makefile
-+++ b/src/jaccard/Makefile
-@@ -43,7 +43,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/linksBed/Makefile
-+++ b/src/linksBed/Makefile
-@@ -25,7 +25,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/mapFile/Makefile
-+++ b/src/mapFile/Makefile
-@@ -38,7 +38,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/maskFastaFromBed/Makefile
-+++ b/src/maskFastaFromBed/Makefile
-@@ -25,7 +25,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/mergeFile/Makefile
-+++ b/src/mergeFile/Makefile
-@@ -40,7 +40,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/multiBamCov/Makefile
-+++ b/src/multiBamCov/Makefile
-@@ -26,7 +26,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/multiIntersectBed/Makefile
-+++ b/src/multiIntersectBed/Makefile
-@@ -27,7 +27,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/nekSandbox1/Makefile
-+++ b/src/nekSandbox1/Makefile
-@@ -35,7 +35,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/nucBed/Makefile
-+++ b/src/nucBed/Makefile
-@@ -27,7 +27,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/pairToBed/Makefile
-+++ b/src/pairToBed/Makefile
-@@ -27,7 +27,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/pairToPair/Makefile
-+++ b/src/pairToPair/Makefile
-@@ -27,7 +27,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
-
- clean:
---- a/src/randomBed/Makefile
-+++ b/src/randomBed/Makefile
-@@ -23,7 +23,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/regressTest/Makefile
-+++ b/src/regressTest/Makefile
-@@ -24,24 +24,18 @@
- # ----------------------------------
- # define our source and object files
- # ----------------------------------
--#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
--#OBJECTS= regressTestMain.o RegressTest.o
--#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
-+SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h
-+OBJECTS= regressTestMain.o RegressTest.o
-+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
- PROGRAM= regressTest
-
--
--all: #$(BUILT_OBJECTS)
-- @echo "compiling RegressTest.cpp"
-- @$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-- @echo "compiling regressTestMain.cpp"
-- @$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+all: $(BUILT_OBJECTS)
-
- .PHONY: all
-
--#$(BUILT_OBJECTS): $(SOURCES)
--# @echo " * compiling" $(*F).cpp
--# @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
--
-+$(BUILT_OBJECTS): $(SOURCES)
-+ @echo " * compiling" $(*F).cpp
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/reldist/Makefile
-+++ b/src/reldist/Makefile
-@@ -30,7 +30,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/sampleFile/Makefile
-+++ b/src/sampleFile/Makefile
-@@ -37,7 +37,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/shiftBed/Makefile
-+++ b/src/shiftBed/Makefile
-@@ -26,7 +26,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/shuffleBed/Makefile
-+++ b/src/shuffleBed/Makefile
-@@ -28,7 +28,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/slopBed/Makefile
-+++ b/src/slopBed/Makefile
-@@ -26,7 +26,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/sortBed/Makefile
-+++ b/src/sortBed/Makefile
-@@ -26,7 +26,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/spacingFile/Makefile
-+++ b/src/spacingFile/Makefile
-@@ -37,7 +37,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/split/Makefile
-+++ b/src/split/Makefile
-@@ -25,7 +25,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/subtractFile/Makefile
-+++ b/src/subtractFile/Makefile
-@@ -40,7 +40,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/tagBam/Makefile
-+++ b/src/tagBam/Makefile
-@@ -28,7 +28,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/unionBedGraphs/Makefile
-+++ b/src/unionBedGraphs/Makefile
-@@ -27,7 +27,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/BamTools/Makefile
-+++ b/src/utils/BamTools/Makefile
-@@ -56,12 +56,12 @@
-
- $(LIBRARY): $(OBJECTS)
- @echo " * linking $(LIBRARY)"
-- ar cr $@ $^
-+ $(AR) cr $@ $^
- -ranlib $@
-
- $(OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o -c $(*D)/$(*F).cpp
-
- .PHONY: api
- api:
---- a/src/utils/BamTools-Ancillary/Makefile
-+++ b/src/utils/BamTools-Ancillary/Makefile
-@@ -21,7 +21,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/bedFile/Makefile
-+++ b/src/utils/bedFile/Makefile
-@@ -20,7 +20,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C -W $(INCLUDES)
---- a/src/utils/bedFilePE/Makefile
-+++ b/src/utils/bedFilePE/Makefile
-@@ -17,7 +17,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/bedGraphFile/Makefile
-+++ b/src/utils/bedGraphFile/Makefile
-@@ -19,7 +19,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C -W $(INCLUDES)
---- a/src/utils/BinTree/Makefile
-+++ b/src/utils/BinTree/Makefile
-@@ -28,7 +28,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/BlockedIntervals/Makefile
-+++ b/src/utils/BlockedIntervals/Makefile
-@@ -23,7 +23,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/chromsweep/Makefile
-+++ b/src/utils/chromsweep/Makefile
-@@ -20,7 +20,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/Contexts/Makefile
-+++ b/src/utils/Contexts/Makefile
-@@ -36,7 +36,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/driver/Makefile
-+++ b/src/utils/driver/Makefile
-@@ -85,7 +85,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/Fasta/Makefile
-+++ b/src/utils/Fasta/Makefile
-@@ -19,7 +19,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/FileRecordTools/FileReaders/Makefile
-+++ b/src/utils/FileRecordTools/FileReaders/Makefile
-@@ -32,7 +32,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/FileRecordTools/FileReaders/Makefile~
-+++ b/src/utils/FileRecordTools/FileReaders/Makefile~
-@@ -31,7 +31,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/FileRecordTools/Makefile
-+++ b/src/utils/FileRecordTools/Makefile
-@@ -34,9 +34,9 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling FileRecordMgr.cpp"
-- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp
- @echo " * compiling FileRecordMergeMgr.cpp"
-- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp
-
-
-
---- a/src/utils/FileRecordTools/Records/Makefile
-+++ b/src/utils/FileRecordTools/Records/Makefile
-@@ -37,7 +37,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/fileType/Makefile
-+++ b/src/utils/fileType/Makefile
-@@ -22,7 +22,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/general/Makefile
-+++ b/src/utils/general/Makefile
-@@ -21,7 +21,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/GenomeFile/Makefile
-+++ b/src/utils/GenomeFile/Makefile
-@@ -20,9 +20,9 @@
-
- $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
- @echo " * compiling GenomeFile.cpp"
-- @$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp
- @echo " * compiling NewGenomeFile.cpp"
-- @$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp
-
- #$(EXT_OBJECTS):
- # @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
---- a/src/utils/gzstream/Makefile
-+++ b/src/utils/gzstream/Makefile
-@@ -38,7 +38,7 @@
- UTILITIES_DIR = ../../utils/
-
- ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h
-- $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/gzstream.o gzstream.C
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/KeyListOps/Makefile
-+++ b/src/utils/KeyListOps/Makefile
-@@ -31,7 +31,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
-
- $(EXT_OBJECTS):
---- a/src/utils/NewChromsweep/Makefile
-+++ b/src/utils/NewChromsweep/Makefile
-@@ -34,7 +34,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/RecordOutputMgr/Makefile
-+++ b/src/utils/RecordOutputMgr/Makefile
-@@ -29,7 +29,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/sequenceUtilities/Makefile
-+++ b/src/utils/sequenceUtilities/Makefile
-@@ -17,7 +17,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/tabFile/Makefile
-+++ b/src/utils/tabFile/Makefile
-@@ -19,7 +19,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C -W $(INCLUDES)
---- a/src/utils/ToolBase/Makefile
-+++ b/src/utils/ToolBase/Makefile
-@@ -30,7 +30,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(INCLUDES)
---- a/src/utils/VectorOps/Makefile
-+++ b/src/utils/VectorOps/Makefile
-@@ -11,7 +11,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/utils/version/Makefile
-+++ b/src/utils/version/Makefile
-@@ -20,7 +20,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES) $(HEADERS)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/windowBed/Makefile
-+++ b/src/windowBed/Makefile
-@@ -27,7 +27,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- clean:
- @echo "Cleaning up."
---- a/src/windowMaker/Makefile
-+++ b/src/windowMaker/Makefile
-@@ -26,7 +26,7 @@
-
- $(BUILT_OBJECTS): $(SOURCES)
- @echo " * compiling" $(*F).cpp
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES)
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
-
- $(EXT_OBJECTS):
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/
@ 2020-08-16 20:50 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2020-08-16 20:50 UTC (permalink / raw
To: gentoo-commits
commit: 3a1f5a9faf6dfeb828e148cd397290d670c93744
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Aug 16 20:49:49 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Aug 16 20:49:49 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3a1f5a9f
sci-biology/bedtools: Version bump to 2.29.2
Bug: https://bugs.gentoo.org/718468
Package-Manager: Portage-3.0.2, Repoman-2.3.23
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bedtools/Manifest | 1 +
sci-biology/bedtools/bedtools-2.29.2.ebuild | 48 +++++++++++++
.../files/bedtools-2.29.2-buildsystem.patch | 82 ++++++++++++++++++++++
.../bedtools/files/bedtools-2.29.2-python.patch | 41 +++++++++++
.../files/bedtools-2.29.2-samtools-1.10.patch | 13 ++++
5 files changed, 185 insertions(+)
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 642fe852658..d776ef0925a 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,2 +1,3 @@
DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3
DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def
+DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5
diff --git a/sci-biology/bedtools/bedtools-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild
new file mode 100644
index 00000000000..de337827bf2
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.29.2.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+
+inherit python-any-r1 toolchain-funcs
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
+HOMEPAGE="https://bedtools.readthedocs.io/"
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ app-arch/bzip2
+ app-arch/xz-utils
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="test? ( >=sci-biology/samtools-1.10:0 )"
+
+S="${WORKDIR}"/${PN}2
+
+# bedtools2 has a *terrible* build system and development practices.
+# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
+# that make unbundling it nigh impossible. There are no signs of upstream porting
+# their fork to 1.10, which means we're stuck with the bundled version.
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.29.2-buildsystem.patch
+ "${FILESDIR}"/${PN}-2.29.2-python.patch
+ "${FILESDIR}"/${PN}-2.29.2-samtools-1.10.patch
+)
+
+src_configure() {
+ tc-export AR CC CXX RANLIB
+}
+
+src_install() {
+ default
+
+ insinto /usr/share/${PN}
+ doins -r genomes
+}
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
new file mode 100644
index 00000000000..573e88993bc
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
@@ -0,0 +1,82 @@
+--- a/Makefile
++++ b/Makefile
+@@ -4,44 +4,29 @@
+ # (c) 2009 Aaron Quinlan
+ # ==========================
+
+-SHELL := /bin/bash -e
++SHELL := bash -e
+
+ VERSION_FILE=./src/utils/version/version_git.h
+ RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
+
+
+ # define our object and binary directories
+-ifeq ($(VERBOSE),1)
+ CCPREFIX =
+-else
+-CCPREFIX = @
+-endif
+
+ OBJ_DIR = obj
+ BIN_DIR = bin
+ SRC_DIR = src
+
+-CXX = g++
+-
+-ifeq ($(DEBUG),1)
+-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
+-else
+ BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+-BT_CXXFLAGS = -g -Wall -O2
+-endif
++BT_CXXFLAGS = -Wall
+
+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
+-ifeq ($(USE_RAND),1)
+-BT_CXXFLAGS += -DUSE_RAND
+-else
+ BT_CXXFLAGS += -std=c++11
+-endif
+
+ BT_LDFLAGS =
+ BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
+
+-prefix ?= /usr/local
++prefix = $(EPREFIX)/usr
+
+ SUBDIRS = $(SRC_DIR)/annotateBed \
+ $(SRC_DIR)/bamToBed \
+@@ -204,7 +189,7 @@
+
+ # make the "obj/" and "bin/" directories, if they don't exist
+ $(OBJ_DIR) $(BIN_DIR):
+- @mkdir -p $@
++ mkdir -p $@
+
+
+ # Usually HTSlib's configure script has not been used (detected via config.mk
+--- a/src/utils/htslib/Makefile
++++ b/src/utils/htslib/Makefile
+@@ -22,20 +22,13 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+
+-CC = gcc
+-AR = ar
+-RANLIB = ranlib
+-
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma
+
+-CPPFLAGS =
+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+ # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+ #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
+-CFLAGS = -g -Wall -O2
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS =
+ LIBS = $(htslib_default_libs)
+
+ prefix = /usr/local
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-python.patch b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch
new file mode 100644
index 00000000000..9576a78bd1d
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch
@@ -0,0 +1,41 @@
+--- a/Makefile
++++ b/Makefile
+@@ -183,7 +168,7 @@
+
+ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+ @echo "- Creating executables for old CLI."
+- @python scripts/makeBashScripts.py
++ $(EPYTHON) scripts/makeBashScripts.py
+ @chmod +x bin/*
+ @echo "done."
+
+--- a/src/utils/BamTools/Makefile.frag
++++ b/src/utils/BamTools/Makefile.frag
+@@ -1,4 +1,4 @@
+ src/utils/BamTools/include/BamAlignment.mapping.hpp: src/utils/BamTools/mapping/BamAlignment.py src/utils/BamTools/mapping/BamAlignment.map
+
+ src/utils/BamTools/include/%.mapping.hpp: src/utils/BamTools/mapping/%.py src/utils/BamTools/mapping/%.map
+- python $^ > $@
++ $(EPYTHON) $^ > $@
+--- a/test/bigchroms/test-bigchroms.sh
++++ b/test/bigchroms/test-bigchroms.sh
+@@ -28,7 +28,7 @@
+ rm obs
+
+ if [[ "$BT_NO_BIG_FILES" != "" ]]; then
+-python make-big-chrom.py
++${EPYTHON} make-big-chrom.py
+
+ echo -e " bigchroms.t03...big get fasta \c"
+ $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
+--- a/test/fisher/cmp.sh
++++ b/test/fisher/cmp.sh
+@@ -3,7 +3,7 @@
+ echo "fisher,shuffled"
+
+ for i in $(seq 1000); do
+- fisher=$(python ./sim.py | tail -1 | cut -f 2)
++ fisher=$(${EPYTHON} ./sim.py | tail -1 | cut -f 2)
+ shuffle=$(bash shuf.sh)
+ echo "$fisher,$shuffle"
+ done
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
new file mode 100644
index 00000000000..7cc0e23de2d
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
@@ -0,0 +1,13 @@
+--- a/test/intersect/new_test-intersect.sh
++++ b/test/intersect/new_test-intersect.sh
+@@ -975,8 +975,8 @@
+ # Test intersect preserve the text header in bam
+ ############################################################
+ echo -e " intersect.new.t78...\c"
+-echo -e "@HD VN:1.5 SO:coordinate" > exp
+-echo "@HD VN:1.5 SO:coordinate" | samtools view -b | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs
++echo -e "@HD VN:1.5 SO:coordinate" > exp
++echo "@HD VN:1.5 SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs
+ check exp obs
+ rm exp obs
+ [[ $FAILURES -eq 0 ]] || exit 1;
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/
@ 2022-03-19 11:38 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2022-03-19 11:38 UTC (permalink / raw
To: gentoo-commits
commit: 668ca73d47c048362cec2674c3bced215423a533
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 19 11:38:06 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 19 11:38:06 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=668ca73d
sci-biology/bedtools: drop 2.29.2
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bedtools/Manifest | 1 -
sci-biology/bedtools/bedtools-2.29.2.ebuild | 50 ----------------------
.../files/bedtools-2.29.2-samtools-1.10.patch | 13 ------
3 files changed, 64 deletions(-)
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index d2d1a7150f72..571c4c92d6b5 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,2 +1 @@
-DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5
DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9
diff --git a/sci-biology/bedtools/bedtools-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild
deleted file mode 100644
index c90bc512fe34..000000000000
--- a/sci-biology/bedtools/bedtools-2.29.2.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit python-any-r1 toolchain-funcs
-
-DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
-HOMEPAGE="https://bedtools.readthedocs.io/"
-SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- app-arch/bzip2
- app-arch/xz-utils
- sys-libs/zlib"
-DEPEND="${RDEPEND}"
-BDEPEND="
- ${PYTHON_DEPS}
- test? ( >=sci-biology/samtools-1.10:0 )"
-
-S="${WORKDIR}"/${PN}2
-
-# bedtools2 has a *terrible* build system and development practices.
-# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
-# that make unbundling it nigh impossible. There are no signs of upstream porting
-# their fork to 1.10, which means we're stuck with the bundled version.
-PATCHES=(
- "${FILESDIR}"/${PN}-2.29.2-buildsystem.patch
- "${FILESDIR}"/${PN}-2.29.2-python.patch
- "${FILESDIR}"/${PN}-2.29.2-samtools-1.10.patch
-)
-
-src_configure() {
- tc-export AR CC CXX RANLIB
-}
-
-src_install() {
- default
-
- insinto /usr/share/${PN}
- doins -r genomes
-}
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
deleted file mode 100644
index 7cc0e23de2d4..000000000000
--- a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- a/test/intersect/new_test-intersect.sh
-+++ b/test/intersect/new_test-intersect.sh
-@@ -975,8 +975,8 @@
- # Test intersect preserve the text header in bam
- ############################################################
- echo -e " intersect.new.t78...\c"
--echo -e "@HD VN:1.5 SO:coordinate" > exp
--echo "@HD VN:1.5 SO:coordinate" | samtools view -b | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs
-+echo -e "@HD VN:1.5 SO:coordinate" > exp
-+echo "@HD VN:1.5 SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs
- check exp obs
- rm exp obs
- [[ $FAILURES -eq 0 ]] || exit 1;
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/
@ 2023-04-18 10:04 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2023-04-18 10:04 UTC (permalink / raw
To: gentoo-commits
commit: 0f6ed95b2b57ae7f9978b1a3b1620c3dcb06256e
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 18 10:04:37 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Apr 18 10:04:37 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0f6ed95b
sci-biology/bedtools: fix gcc 13 build
Closes: https://bugs.gentoo.org/895860
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bedtools/bedtools-2.30.0.ebuild | 1 +
.../bedtools/files/bedtools-2.30.0-gcc13.patch | 25 ++++++++++++++++++++++
2 files changed, 26 insertions(+)
diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild
index 5a8174fbdfe0..b86b87e72dc4 100644
--- a/sci-biology/bedtools/bedtools-2.30.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild
@@ -34,6 +34,7 @@ BDEPEND="
PATCHES=(
"${FILESDIR}"/${PN}-2.29.2-buildsystem.patch
"${FILESDIR}"/${PN}-2.29.2-python.patch
+ "${FILESDIR}"/${PN}-2.30.0-gcc13.patch
)
src_configure() {
diff --git a/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch
new file mode 100644
index 000000000000..c63faf31c851
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch
@@ -0,0 +1,25 @@
+https://github.com/arq5x/bedtools2/pull/1045
+
+From 7d7fb513b9b05b7a0512a83520e9f60036e5ff9a Mon Sep 17 00:00:00 2001
+From: David Seifert <soap@gentoo.org>
+Date: Tue, 18 Apr 2023 11:59:58 +0200
+Subject: [PATCH] Add missing <cstdint> include
+
+* breaks build with GCC 13:
+ https://bugs.gentoo.org/895860
+---
+ src/utils/general/ParseTools.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h
+index e056c149..3418eff1 100644
+--- a/src/utils/general/ParseTools.h
++++ b/src/utils/general/ParseTools.h
+@@ -16,6 +16,7 @@
+ #include "string.h"
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstdint>
+
+ using namespace std;
+
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/
@ 2024-04-25 9:38 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2024-04-25 9:38 UTC (permalink / raw
To: gentoo-commits
commit: 6659d55f12a3e8b75dbf9545cac23f37ca00bd58
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 25 09:37:47 2024 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Apr 25 09:37:47 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6659d55f
sci-biology/bedtools: add 2.31.1
Bug: https://bugs.gentoo.org/881783
Bug: https://bugs.gentoo.org/907971
Bug: https://bugs.gentoo.org/929751
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bedtools/Manifest | 1 +
sci-biology/bedtools/bedtools-2.31.1.ebuild | 49 ++++++
.../files/bedtools-2.31.1-buildsystem.patch | 84 ++++++++++
.../bedtools/files/bedtools-2.31.1-includes.patch | 178 +++++++++++++++++++++
.../bedtools/files/bedtools-2.31.1-python.patch | 40 +++++
5 files changed, 352 insertions(+)
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 571c4c92d6b5..0b52182a52f6 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1 +1,2 @@
DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9
+DIST bedtools-2.31.1.tar.gz 19629373 BLAKE2B f09742ee74494c783cef4909c56abd7b8542344539fe006140716b0a6a1d972db4e3df4a03fb3996a71cb57709b0494be8686879cba15c0985236f3a1282c92d SHA512 fbdc23011566697b2fc44bf3e7b466949487d3f648e81957fa80e8ad4b192d0ef7e2e3944b9b18612774a7984ec99e3fc339c3fddb8889caa632b8ce8defa20d
diff --git a/sci-biology/bedtools/bedtools-2.31.1.ebuild b/sci-biology/bedtools/bedtools-2.31.1.ebuild
new file mode 100644
index 000000000000..57ee6c3fde3f
--- /dev/null
+++ b/sci-biology/bedtools/bedtools-2.31.1.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+inherit python-any-r1 toolchain-funcs
+
+DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
+HOMEPAGE="https://bedtools.readthedocs.io/"
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
+S="${WORKDIR}/${PN}2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ app-arch/bzip2
+ app-arch/xz-utils
+ sys-libs/zlib"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ ${PYTHON_DEPS}
+ test? ( >=sci-biology/samtools-1.10:0 )"
+
+# bedtools2 has a *terrible* build system and development practices.
+# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
+# that make unbundling it nigh impossible. There are no signs of upstream porting
+# their fork to 1.10, which means we're stuck with the bundled version.
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.31.1-buildsystem.patch
+ "${FILESDIR}"/${PN}-2.31.1-python.patch
+ "${FILESDIR}"/${PN}-2.31.1-includes.patch
+)
+
+src_configure() {
+ tc-export AR CC CXX RANLIB
+}
+
+src_install() {
+ default
+
+ insinto /usr/share/bedtools
+ doins -r genomes
+}
diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch
new file mode 100644
index 000000000000..8bb2a096e917
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.31.1-buildsystem.patch
@@ -0,0 +1,84 @@
+--- a/Makefile
++++ b/Makefile
+@@ -4,46 +4,29 @@
+ # (c) 2009 Aaron Quinlan
+ # ==========================
+
+-SHELL := /bin/bash -e
++SHELL := bash -e
+
+ VERSION_FILE=./src/utils/version/version_git.h
+ RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
+
+
+ # define our object and binary directories
+-ifeq ($(VERBOSE),1)
+ CCPREFIX =
+-else
+-CCPREFIX = @
+-endif
+
+ OBJ_DIR = obj
+ BIN_DIR = bin
+ SRC_DIR = src
+
+-CXX = g++
+-
+-PYTHON ?= $(shell python --version >/dev/null 2>&1 && echo "python" || echo python3)
+-
+-ifeq ($(DEBUG),1)
+-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
+-else
+ BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+-BT_CXXFLAGS = -g -Wall -O2
+-endif
++BT_CXXFLAGS = -Wall
+
+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
+-ifeq ($(USE_RAND),1)
+-BT_CXXFLAGS += -DUSE_RAND
+-else
+ BT_CXXFLAGS += -std=c++11
+-endif
+
+ BT_LDFLAGS =
+ BT_LIBS = -lz -lm -lbz2 -llzma -lpthread
+
+-prefix ?= /usr/local
++prefix = $(EPREFIX)/usr
+
+ SUBDIRS = $(SRC_DIR)/annotateBed \
+ $(SRC_DIR)/bamToBed \
+@@ -213,7 +196,7 @@
+
+ # make the "obj/" and "bin/" directories, if they don't exist
+ $(OBJ_DIR) $(BIN_DIR):
+- @mkdir -p $@
++ mkdir -p $@
+
+
+ # Usually HTSlib's configure script has not been used (detected via config.mk
+--- a/src/utils/htslib/Makefile
++++ b/src/utils/htslib/Makefile
+@@ -22,20 +22,13 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+
+-CC = gcc
+-AR = ar
+-RANLIB = ranlib
+-
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma
+
+-CPPFLAGS =
+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+ # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+ #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
+-CFLAGS = -g -Wall -O2
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS =
+ LIBS = $(htslib_default_libs)
+
+ prefix = /usr/local
diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch
new file mode 100644
index 000000000000..1b0a9f0849ed
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.31.1-includes.patch
@@ -0,0 +1,178 @@
+From 3fbf2ddc8ebf0fc1bd492d14a6046aadd59ecadb Mon Sep 17 00:00:00 2001
+From: David Seifert <soap@gentoo.org>
+Date: Thu, 25 Apr 2024 11:18:48 +0200
+Subject: [PATCH] Add missing `stdint.h` includes
+
+* Musl is a lot stricter with transitive includes:
+ Bug: https://bugs.gentoo.org/907971
+--- a/src/bamToBed/bamToBed.cpp
++++ b/src/bamToBed/bamToBed.cpp
+@@ -22,6 +22,7 @@ using namespace BamTools;
+ #include <sstream>
+ #include <fstream>
+ #include <stdlib.h>
++#include <stdint.h>
+
+ using namespace std;
+
+--- a/src/clusterBed/clusterBed.cpp
++++ b/src/clusterBed/clusterBed.cpp
+@@ -12,6 +12,8 @@
+ #include "lineFileUtilities.h"
+ #include "clusterBed.h"
+
++#include <stdint.h>
++
+ // = Constructor =
+ BedCluster::BedCluster(string &bedFile,
+ int maxDistance,
+--- a/src/pairToBed/pairToBed.h
++++ b/src/pairToBed/pairToBed.h
+@@ -22,6 +22,7 @@ using namespace BamTools;
+ #include <vector>
+ #include <iostream>
+ #include <fstream>
++#include <stdint.h>
+
+ using namespace std;
+
+--- a/src/randomBed/randomBed.h
++++ b/src/randomBed/randomBed.h
+@@ -22,6 +22,7 @@
+ #include <unistd.h>
+ #include <sys/types.h>
+ #include <algorithm> // for binary search
++#include <stdint.h>
+ using namespace std;
+
+ const int MAX_TRIES = 1000000;
+--- a/src/summaryFile/summaryFile.h
++++ b/src/summaryFile/summaryFile.h
+@@ -12,6 +12,8 @@
+ #include "ToolBase.h"
+ #include "ContextSummary.h"
+
++#include <stdint.h>
++
+ struct Interval {
+ CHRPOS start;
+ CHRPOS end;
+--- a/src/utils/BamTools/include/BamAlignment.mapping.hpp
++++ b/src/utils/BamTools/include/BamAlignment.mapping.hpp
+@@ -1,3 +1,4 @@
++#include <stdint.h>
+
+ struct _RefID_t {
+ operator int32_t() const {return (int32_t)(_ptr()->core.tid);}
+--- a/src/utils/BamTools/include/api/BamAux.h
++++ b/src/utils/BamTools/include/api/BamAux.h
+@@ -1,4 +1,5 @@
+ #include <string>
++#include <stdint.h>
+
+ #ifndef BAMAUX_H
+ #define BAMAUX_H
+--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
++++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
+@@ -9,6 +9,7 @@
+ #define SINGLELINETEXTFILEREADER_H_
+
+ #include <algorithm>
++#include <stdint.h>
+ #include "FileReader.h"
+ #include "string.h"
+ #include "lineFileUtilities.h"
+--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
++++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
+@@ -10,6 +10,8 @@
+ #include "BamFileReader.h"
+ #include "RecordKeyVector.h"
+
++#include <stdint.h>
++
+ BamRecord::BamRecord()
+ : _bamChromId(-1)
+ {
+--- a/src/utils/GenomeFile/GenomeFile.h
++++ b/src/utils/GenomeFile/GenomeFile.h
+@@ -19,6 +19,7 @@
+ #include <fstream>
+ #include <cstring>
+ #include <cstdio>
++#include <stdint.h>
+ #include <algorithm> // for bsearch lower_bound()
+ #include "api/BamReader.h"
+ #include "api/BamAux.h"
+--- a/src/utils/GenomeFile/NewGenomeFile.h
++++ b/src/utils/GenomeFile/NewGenomeFile.h
+@@ -14,6 +14,7 @@
+ #define NEW_GENOMEFILE_H
+
+ #include <algorithm> // for bsearch lower_bound()
++#include <stdint.h>
+
+ #include "BedtoolsTypes.h"
+
+--- a/src/utils/bedFilePE/bedFilePE.h
++++ b/src/utils/bedFilePE/bedFilePE.h
+@@ -8,6 +8,7 @@
+ #include <fstream>
+ #include <sstream>
+ #include <cstring>
++#include <stdint.h>
+ #include <algorithm>
+ #include "bedFile.h"
+ #include "lineFileUtilities.h"
+--- a/src/utils/general/ParseTools.cpp
++++ b/src/utils/general/ParseTools.cpp
+@@ -2,7 +2,7 @@
+ #include <climits>
+ #include <cctype>
+ #include <cstring>
+-#include <cstdint>
++#include <stdint.h>
+ #include <cstdio>
+ #include <cstdlib>
+ #include <sstream>
+--- a/src/utils/lineFileUtilities/lineFileUtilities.h
++++ b/src/utils/lineFileUtilities/lineFileUtilities.h
+@@ -4,6 +4,7 @@
+ #include <vector>
+ #include <string>
+ #include <cstring>
++#include <stdint.h>
+ #include <cstdlib>
+ #include <sstream>
+ #include <iostream>
+--- a/src/utils/sequenceUtilities/sequenceUtils.h
++++ b/src/utils/sequenceUtilities/sequenceUtils.h
+@@ -4,6 +4,7 @@
+ #include <string>
+ #include <algorithm>
+ #include <cctype>
++#include <stdint.h>
+
+ using namespace std;
+
+--- a/src/windowMaker/windowMaker.h
++++ b/src/windowMaker/windowMaker.h
+@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
+ #include "NewGenomeFile.h"
+ #include "bedFile.h"
+
++#include <stdint.h>
++
+ using namespace std;
+
+
+--- a/src/windowMaker/windowMakerMain.cpp
++++ b/src/windowMaker/windowMakerMain.cpp
+@@ -12,6 +12,8 @@ Licenced under the GNU General Public License 2.0 license.
+ #include "windowMaker.h"
+ #include "version.h"
+
++#include <stdint.h>
++
+ using namespace std;
+
+ // define our program name
diff --git a/sci-biology/bedtools/files/bedtools-2.31.1-python.patch b/sci-biology/bedtools/files/bedtools-2.31.1-python.patch
new file mode 100644
index 000000000000..28819ac82d49
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.31.1-python.patch
@@ -0,0 +1,40 @@
+From eabcd3dcb9caa1fcc17acd43df2ded4170ed1449 Mon Sep 17 00:00:00 2001
+From: David Seifert <soap@gentoo.org>
+Date: Thu, 25 Apr 2024 11:18:47 +0200
+Subject: [PATCH] Allow PYTHON from environment
+
+* Distros need to be able to specify exactly which python
+ interpreter to run tests under.
+--- a/test/bigchroms/test-bigchroms.sh
++++ b/test/bigchroms/test-bigchroms.sh
+@@ -28,7 +28,7 @@ check obs abig.bed
+ rm obs
+
+ if [[ "$BT_NO_BIG_FILES" != "" ]]; then
+-python make-big-chrom.py
++${PYTHON:-python} make-big-chrom.py
+
+ echo -e " bigchroms.t03...big get fasta \c"
+ $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
+--- a/test/fisher/cmp.sh
++++ b/test/fisher/cmp.sh
+@@ -3,7 +3,7 @@ set -eo pipefail
+ echo "fisher,shuffled"
+
+ for i in $(seq 1000); do
+- fisher=$(python ./sim.py | tail -1 | cut -f 2)
++ fisher=$(${PYTHON:-python} ./sim.py | tail -1 | cut -f 2)
+ shuffle=$(bash shuf.sh)
+ echo "$fisher,$shuffle"
+ done
+--- a/test/genomecov/test-genomecov.sh
++++ b/test/genomecov/test-genomecov.sh
+@@ -288,7 +288,7 @@ CRAM_REFERENCE=test_ref.fa $BT genomecov -ibam empty.cram > obs
+ check obs exp
+ rm obs exp
+
+-python mk-deep.py > deep.sam
++${PYTHON:-python} mk-deep.py > deep.sam
+ echo -e " genomecov.t18...\c"
+ echo "c1 1 1000000" > exp
+ $BT genomecov -d -ibam deep.sam | head -1 > obs
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2017-12-10 0:05 [gentoo-commits] repo/gentoo:master commit in: sci-biology/bedtools/files/, sci-biology/bedtools/ Michał Górny
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