| 1 |
commit: 96adca668f64cdeb561fab922e1489e8f5aa01de |
| 2 |
Author: Michał Górny <mgorny <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Sat Dec 9 23:15:36 2017 +0000 |
| 4 |
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Sun Dec 10 00:05:27 2017 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=96adca66 |
| 7 |
|
| 8 |
sci-biology/bedtools: [QA] Move patch to a distfile |
| 9 |
|
| 10 |
Closes: https://bugs.gentoo.org/620612 |
| 11 |
|
| 12 |
sci-biology/bedtools/Manifest | 3 +- |
| 13 |
sci-biology/bedtools/bedtools-2.26.0.ebuild | 7 +- |
| 14 |
.../files/bedtools-2.26.0-fix-buildsystem.patch | 869 --------------------- |
| 15 |
3 files changed, 6 insertions(+), 873 deletions(-) |
| 16 |
|
| 17 |
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest |
| 18 |
index e398b3bee6f..642fe852658 100644 |
| 19 |
--- a/sci-biology/bedtools/Manifest |
| 20 |
+++ b/sci-biology/bedtools/Manifest |
| 21 |
@@ -1 +1,2 @@ |
| 22 |
-DIST bedtools-2.26.0.tar.gz 19939711 SHA256 65f32f32cbf1b91ba42854b40c604aa6a16c7d3b3ec110d6acf438eb22df0a4a SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def WHIRLPOOL 8d6e3b58dc38d7ab91482ffe5ee773953864ca79bdbf005b17fec51952a869b39bf775d836ed34496a7784565bb84380eef284e285e842d52229fe2fc6a214b2 |
| 23 |
+DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3 |
| 24 |
+DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def |
| 25 |
|
| 26 |
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild |
| 27 |
index eeedf606deb..0520143f3d9 100644 |
| 28 |
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild |
| 29 |
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild |
| 30 |
@@ -1,4 +1,4 @@ |
| 31 |
-# Copyright 1999-2016 Gentoo Foundation |
| 32 |
+# Copyright 1999-2017 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
| 34 |
|
| 35 |
EAPI=6 |
| 36 |
@@ -9,7 +9,8 @@ inherit flag-o-matic python-any-r1 toolchain-funcs |
| 37 |
|
| 38 |
DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" |
| 39 |
HOMEPAGE="https://bedtools.readthedocs.io/" |
| 40 |
-SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" |
| 41 |
+SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz |
| 42 |
+ https://dev.gentoo.org/~mgorny/dist/${PN}-2.26.0-fix-buildsystem.patch.bz2" |
| 43 |
|
| 44 |
LICENSE="GPL-2" |
| 45 |
SLOT="0" |
| 46 |
@@ -26,7 +27,7 @@ RDEPEND="sys-libs/zlib" |
| 47 |
S="${WORKDIR}/${PN}2" |
| 48 |
|
| 49 |
DOCS=( README.md RELEASE_HISTORY ) |
| 50 |
-PATCHES=( "${FILESDIR}/${PN}-2.26.0-fix-buildsystem.patch" ) |
| 51 |
+PATCHES=( "${WORKDIR}/${PN}-2.26.0-fix-buildsystem.patch" ) |
| 52 |
|
| 53 |
src_configure() { |
| 54 |
append-lfs-flags |
| 55 |
|
| 56 |
diff --git a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch |
| 57 |
deleted file mode 100644 |
| 58 |
index fb6be18d707..00000000000 |
| 59 |
--- a/sci-biology/bedtools/files/bedtools-2.26.0-fix-buildsystem.patch |
| 60 |
+++ /dev/null |
| 61 |
@@ -1,869 +0,0 @@ |
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-* Make build system verbose (https://bugs.gentoo.org/show_bug.cgi?id=429308) |
| 63 |
-* Remove CXX and CXXFLAGS, ebuild sets them |
| 64 |
-* Handle python via Gentoo's EPYTHON instead |
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- |
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---- a/Makefile |
| 67 |
-+++ b/Makefile |
| 68 |
-@@ -16,17 +16,9 @@ |
| 69 |
- export BIN_DIR = bin |
| 70 |
- export SRC_DIR = src |
| 71 |
- export UTIL_DIR = src/utils |
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--export CXX = g++ |
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--ifeq ($(DEBUG),1) |
| 74 |
--export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG |
| 75 |
--else |
| 76 |
--export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES) |
| 77 |
--endif |
| 78 |
- export LIBS = -lz |
| 79 |
- export BT_ROOT = src/utils/BamTools/ |
| 80 |
- |
| 81 |
--prefix ?= /usr/local |
| 82 |
-- |
| 83 |
- SUBDIRS = $(SRC_DIR)/annotateBed \ |
| 84 |
- $(SRC_DIR)/bamToBed \ |
| 85 |
- $(SRC_DIR)/bamToFastq \ |
| 86 |
-@@ -135,13 +127,13 @@ |
| 87 |
- |
| 88 |
- all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS) |
| 89 |
- @echo "- Building main bedtools binary." |
| 90 |
-- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) |
| 91 |
-- @$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES) |
| 92 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES) |
| 93 |
-+ $(CXX) $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) |
| 94 |
- @echo "done." |
| 95 |
- |
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- @echo "- Creating executables for old CLI." |
| 97 |
-- @python scripts/makeBashScripts.py |
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-- @chmod +x bin/* |
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-+ $(EPYTHON) scripts/makeBashScripts.py |
| 100 |
-+ chmod +x bin/* |
| 101 |
- @echo "done." |
| 102 |
- |
| 103 |
- |
| 104 |
---- a/src/annotateBed/Makefile |
| 105 |
-+++ b/src/annotateBed/Makefile |
| 106 |
-@@ -26,7 +26,7 @@ |
| 107 |
- |
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- $(BUILT_OBJECTS): $(SOURCES) |
| 109 |
- @echo " * compiling" $(*F).cpp |
| 110 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 111 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 112 |
- |
| 113 |
- |
| 114 |
- clean: |
| 115 |
---- a/src/bamToBed/Makefile |
| 116 |
-+++ b/src/bamToBed/Makefile |
| 117 |
-@@ -28,7 +28,7 @@ |
| 118 |
- |
| 119 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 120 |
- @echo " * compiling" $(*F).cpp |
| 121 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 122 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 123 |
- |
| 124 |
- clean: |
| 125 |
- @echo "Cleaning up." |
| 126 |
---- a/src/bamToFastq/Makefile |
| 127 |
-+++ b/src/bamToFastq/Makefile |
| 128 |
-@@ -24,7 +24,7 @@ |
| 129 |
- |
| 130 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 131 |
- @echo " * compiling" $(*F).cpp |
| 132 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 133 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 134 |
- |
| 135 |
- clean: |
| 136 |
- @echo "Cleaning up." |
| 137 |
---- a/src/bed12ToBed6/Makefile |
| 138 |
-+++ b/src/bed12ToBed6/Makefile |
| 139 |
-@@ -27,7 +27,7 @@ |
| 140 |
- |
| 141 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 142 |
- @echo " * compiling" $(*F).cpp |
| 143 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 144 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 145 |
- |
| 146 |
- clean: |
| 147 |
- @echo "Cleaning up." |
| 148 |
---- a/src/bedpeToBam/Makefile |
| 149 |
-+++ b/src/bedpeToBam/Makefile |
| 150 |
-@@ -33,7 +33,7 @@ |
| 151 |
- |
| 152 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 153 |
- @echo " * compiling" $(*F).cpp |
| 154 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 155 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 156 |
- |
| 157 |
- $(EXT_OBJECTS): |
| 158 |
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/ |
| 159 |
---- a/src/bedToBam/Makefile |
| 160 |
-+++ b/src/bedToBam/Makefile |
| 161 |
-@@ -30,7 +30,7 @@ |
| 162 |
- |
| 163 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 164 |
- @echo " * compiling" $(*F).cpp |
| 165 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 166 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 167 |
- |
| 168 |
- clean: |
| 169 |
- @echo "Cleaning up." |
| 170 |
---- a/src/bedToIgv/Makefile |
| 171 |
-+++ b/src/bedToIgv/Makefile |
| 172 |
-@@ -28,7 +28,7 @@ |
| 173 |
- |
| 174 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 175 |
- @echo " * compiling" $(*F).cpp |
| 176 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 177 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 178 |
- |
| 179 |
- clean: |
| 180 |
- @echo "Cleaning up." |
| 181 |
---- a/src/closestFile/Makefile |
| 182 |
-+++ b/src/closestFile/Makefile |
| 183 |
-@@ -40,7 +40,7 @@ |
| 184 |
- |
| 185 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 186 |
- @echo " * compiling" $(*F).cpp |
| 187 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 188 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 189 |
- |
| 190 |
- clean: |
| 191 |
- @echo "Cleaning up." |
| 192 |
---- a/src/clusterBed/Makefile |
| 193 |
-+++ b/src/clusterBed/Makefile |
| 194 |
-@@ -25,7 +25,7 @@ |
| 195 |
- |
| 196 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 197 |
- @echo " * compiling" $(*F).cpp |
| 198 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 199 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 200 |
- |
| 201 |
- clean: |
| 202 |
- @echo "Cleaning up." |
| 203 |
---- a/src/complementFile/Makefile |
| 204 |
-+++ b/src/complementFile/Makefile |
| 205 |
-@@ -42,7 +42,7 @@ |
| 206 |
- |
| 207 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 208 |
- @echo " * compiling" $(*F).cpp |
| 209 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) |
| 210 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 211 |
- |
| 212 |
- clean: |
| 213 |
- @echo "Cleaning up." |
| 214 |
---- a/src/coverageFile/Makefile |
| 215 |
-+++ b/src/coverageFile/Makefile |
| 216 |
-@@ -38,7 +38,7 @@ |
| 217 |
- |
| 218 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 219 |
- @echo " * compiling" $(*F).cpp |
| 220 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) |
| 221 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 222 |
- |
| 223 |
- clean: |
| 224 |
- @echo "Cleaning up." |
| 225 |
---- a/src/expand/Makefile |
| 226 |
-+++ b/src/expand/Makefile |
| 227 |
-@@ -27,7 +27,7 @@ |
| 228 |
- |
| 229 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 230 |
- @echo " * compiling" $(*F).cpp |
| 231 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 232 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 233 |
- |
| 234 |
- clean: |
| 235 |
- @echo "Cleaning up." |
| 236 |
---- a/src/fastaFromBed/Makefile |
| 237 |
-+++ b/src/fastaFromBed/Makefile |
| 238 |
-@@ -30,7 +30,7 @@ |
| 239 |
- |
| 240 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 241 |
- @echo " * compiling" $(*F).cpp |
| 242 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 243 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 244 |
- |
| 245 |
- clean: |
| 246 |
- @echo "Cleaning up." |
| 247 |
---- a/src/fisher/Makefile |
| 248 |
-+++ b/src/fisher/Makefile |
| 249 |
-@@ -51,7 +51,7 @@ |
| 250 |
- |
| 251 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 252 |
- @echo " * compiling" $(*F).cpp |
| 253 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) |
| 254 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 255 |
- |
| 256 |
- clean: |
| 257 |
- @echo "Cleaning up." |
| 258 |
---- a/src/flankBed/Makefile |
| 259 |
-+++ b/src/flankBed/Makefile |
| 260 |
-@@ -26,7 +26,7 @@ |
| 261 |
- |
| 262 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 263 |
- @echo " * compiling" $(*F).cpp |
| 264 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 265 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 266 |
- |
| 267 |
- clean: |
| 268 |
- @echo "Cleaning up." |
| 269 |
---- a/src/genomeCoverageBed/Makefile |
| 270 |
-+++ b/src/genomeCoverageBed/Makefile |
| 271 |
-@@ -27,7 +27,7 @@ |
| 272 |
- |
| 273 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 274 |
- @echo " * compiling" $(*F).cpp |
| 275 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 276 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 277 |
- |
| 278 |
- clean: |
| 279 |
- @echo "Cleaning up." |
| 280 |
---- a/src/getOverlap/Makefile |
| 281 |
-+++ b/src/getOverlap/Makefile |
| 282 |
-@@ -26,7 +26,7 @@ |
| 283 |
- |
| 284 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 285 |
- @echo " * compiling" $(*F).cpp |
| 286 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 287 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 288 |
- |
| 289 |
- |
| 290 |
- clean: |
| 291 |
---- a/src/groupBy/Makefile |
| 292 |
-+++ b/src/groupBy/Makefile |
| 293 |
-@@ -42,7 +42,7 @@ |
| 294 |
- |
| 295 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 296 |
- @echo " * compiling" $(*F).cpp |
| 297 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 298 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 299 |
- |
| 300 |
- clean: |
| 301 |
- @echo "Cleaning up." |
| 302 |
---- a/src/intersectFile/Makefile |
| 303 |
-+++ b/src/intersectFile/Makefile |
| 304 |
-@@ -39,7 +39,7 @@ |
| 305 |
- |
| 306 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 307 |
- @echo " * compiling" $(*F).cpp |
| 308 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) |
| 309 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 310 |
- |
| 311 |
- clean: |
| 312 |
- @echo "Cleaning up." |
| 313 |
---- a/src/jaccard/Makefile |
| 314 |
-+++ b/src/jaccard/Makefile |
| 315 |
-@@ -43,7 +43,7 @@ |
| 316 |
- |
| 317 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 318 |
- @echo " * compiling" $(*F).cpp |
| 319 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) |
| 320 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 321 |
- |
| 322 |
- clean: |
| 323 |
- @echo "Cleaning up." |
| 324 |
---- a/src/linksBed/Makefile |
| 325 |
-+++ b/src/linksBed/Makefile |
| 326 |
-@@ -25,7 +25,7 @@ |
| 327 |
- |
| 328 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 329 |
- @echo " * compiling" $(*F).cpp |
| 330 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 331 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 332 |
- |
| 333 |
- clean: |
| 334 |
- @echo "Cleaning up." |
| 335 |
---- a/src/mapFile/Makefile |
| 336 |
-+++ b/src/mapFile/Makefile |
| 337 |
-@@ -38,7 +38,7 @@ |
| 338 |
- |
| 339 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 340 |
- @echo " * compiling" $(*F).cpp |
| 341 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) |
| 342 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 343 |
- |
| 344 |
- clean: |
| 345 |
- @echo "Cleaning up." |
| 346 |
---- a/src/maskFastaFromBed/Makefile |
| 347 |
-+++ b/src/maskFastaFromBed/Makefile |
| 348 |
-@@ -25,7 +25,7 @@ |
| 349 |
- |
| 350 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 351 |
- @echo " * compiling" $(*F).cpp |
| 352 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 353 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 354 |
- |
| 355 |
- clean: |
| 356 |
- @echo "Cleaning up." |
| 357 |
---- a/src/mergeFile/Makefile |
| 358 |
-+++ b/src/mergeFile/Makefile |
| 359 |
-@@ -40,7 +40,7 @@ |
| 360 |
- |
| 361 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 362 |
- @echo " * compiling" $(*F).cpp |
| 363 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 364 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 365 |
- |
| 366 |
- clean: |
| 367 |
- @echo "Cleaning up." |
| 368 |
---- a/src/multiBamCov/Makefile |
| 369 |
-+++ b/src/multiBamCov/Makefile |
| 370 |
-@@ -26,7 +26,7 @@ |
| 371 |
- |
| 372 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 373 |
- @echo " * compiling" $(*F).cpp |
| 374 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 375 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 376 |
- |
| 377 |
- clean: |
| 378 |
- @echo "Cleaning up." |
| 379 |
---- a/src/multiIntersectBed/Makefile |
| 380 |
-+++ b/src/multiIntersectBed/Makefile |
| 381 |
-@@ -27,7 +27,7 @@ |
| 382 |
- |
| 383 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 384 |
- @echo " * compiling" $(*F).cpp |
| 385 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 386 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 387 |
- |
| 388 |
- clean: |
| 389 |
- @echo "Cleaning up." |
| 390 |
---- a/src/nekSandbox1/Makefile |
| 391 |
-+++ b/src/nekSandbox1/Makefile |
| 392 |
-@@ -35,7 +35,7 @@ |
| 393 |
- |
| 394 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 395 |
- @echo " * compiling" $(*F).cpp |
| 396 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) |
| 397 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 398 |
- |
| 399 |
- clean: |
| 400 |
- @echo "Cleaning up." |
| 401 |
---- a/src/nucBed/Makefile |
| 402 |
-+++ b/src/nucBed/Makefile |
| 403 |
-@@ -27,7 +27,7 @@ |
| 404 |
- |
| 405 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 406 |
- @echo " * compiling" $(*F).cpp |
| 407 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 408 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 409 |
- |
| 410 |
- clean: |
| 411 |
- @echo "Cleaning up." |
| 412 |
---- a/src/pairToBed/Makefile |
| 413 |
-+++ b/src/pairToBed/Makefile |
| 414 |
-@@ -27,7 +27,7 @@ |
| 415 |
- |
| 416 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 417 |
- @echo " * compiling" $(*F).cpp |
| 418 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 419 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 420 |
- |
| 421 |
- clean: |
| 422 |
- @echo "Cleaning up." |
| 423 |
---- a/src/pairToPair/Makefile |
| 424 |
-+++ b/src/pairToPair/Makefile |
| 425 |
-@@ -27,7 +27,7 @@ |
| 426 |
- |
| 427 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 428 |
- @echo " * compiling" $(*F).cpp |
| 429 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 430 |
-+ $(CXX) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 431 |
- |
| 432 |
- |
| 433 |
- clean: |
| 434 |
---- a/src/randomBed/Makefile |
| 435 |
-+++ b/src/randomBed/Makefile |
| 436 |
-@@ -23,7 +23,7 @@ |
| 437 |
- |
| 438 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 439 |
- @echo " * compiling" $(*F).cpp |
| 440 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 441 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 442 |
- |
| 443 |
- clean: |
| 444 |
- @echo "Cleaning up." |
| 445 |
---- a/src/regressTest/Makefile |
| 446 |
-+++ b/src/regressTest/Makefile |
| 447 |
-@@ -24,24 +24,18 @@ |
| 448 |
- # ---------------------------------- |
| 449 |
- # define our source and object files |
| 450 |
- # ---------------------------------- |
| 451 |
--#SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h |
| 452 |
--#OBJECTS= regressTestMain.o RegressTest.o |
| 453 |
--#BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) |
| 454 |
-+SOURCES= regressTestMain.cpp RegressTest.cpp RegressTest.h |
| 455 |
-+OBJECTS= regressTestMain.o RegressTest.o |
| 456 |
-+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS)) |
| 457 |
- PROGRAM= regressTest |
| 458 |
- |
| 459 |
-- |
| 460 |
--all: #$(BUILT_OBJECTS) |
| 461 |
-- @echo "compiling RegressTest.cpp" |
| 462 |
-- @$(CXX) -c -o $(OBJ_DIR)/RegressTest.o RegressTest.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 463 |
-- @echo "compiling regressTestMain.cpp" |
| 464 |
-- @$(CXX) -c -o $(OBJ_DIR)/regressTestMain.o regressTestMain.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 465 |
-+all: $(BUILT_OBJECTS) |
| 466 |
- |
| 467 |
- .PHONY: all |
| 468 |
- |
| 469 |
--#$(BUILT_OBJECTS): $(SOURCES) |
| 470 |
--# @echo " * compiling" $(*F).cpp |
| 471 |
--# @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 472 |
-- |
| 473 |
-+$(BUILT_OBJECTS): $(SOURCES) |
| 474 |
-+ @echo " * compiling" $(*F).cpp |
| 475 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 476 |
- |
| 477 |
- clean: |
| 478 |
- @echo "Cleaning up." |
| 479 |
---- a/src/reldist/Makefile |
| 480 |
-+++ b/src/reldist/Makefile |
| 481 |
-@@ -30,7 +30,7 @@ |
| 482 |
- |
| 483 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 484 |
- @echo " * compiling" $(*F).cpp |
| 485 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) |
| 486 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 487 |
- |
| 488 |
- clean: |
| 489 |
- @echo "Cleaning up." |
| 490 |
---- a/src/sampleFile/Makefile |
| 491 |
-+++ b/src/sampleFile/Makefile |
| 492 |
-@@ -37,7 +37,7 @@ |
| 493 |
- |
| 494 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 495 |
- @echo " * compiling" $(*F).cpp |
| 496 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) |
| 497 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 498 |
- |
| 499 |
- clean: |
| 500 |
- @echo "Cleaning up." |
| 501 |
---- a/src/shiftBed/Makefile |
| 502 |
-+++ b/src/shiftBed/Makefile |
| 503 |
-@@ -26,7 +26,7 @@ |
| 504 |
- |
| 505 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 506 |
- @echo " * compiling" $(*F).cpp |
| 507 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 508 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 509 |
- |
| 510 |
- clean: |
| 511 |
- @echo "Cleaning up." |
| 512 |
---- a/src/shuffleBed/Makefile |
| 513 |
-+++ b/src/shuffleBed/Makefile |
| 514 |
-@@ -28,7 +28,7 @@ |
| 515 |
- |
| 516 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 517 |
- @echo " * compiling" $(*F).cpp |
| 518 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 519 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 520 |
- |
| 521 |
- clean: |
| 522 |
- @echo "Cleaning up." |
| 523 |
---- a/src/slopBed/Makefile |
| 524 |
-+++ b/src/slopBed/Makefile |
| 525 |
-@@ -26,7 +26,7 @@ |
| 526 |
- |
| 527 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 528 |
- @echo " * compiling" $(*F).cpp |
| 529 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 530 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 531 |
- |
| 532 |
- clean: |
| 533 |
- @echo "Cleaning up." |
| 534 |
---- a/src/sortBed/Makefile |
| 535 |
-+++ b/src/sortBed/Makefile |
| 536 |
-@@ -26,7 +26,7 @@ |
| 537 |
- |
| 538 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 539 |
- @echo " * compiling" $(*F).cpp |
| 540 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 541 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 542 |
- |
| 543 |
- clean: |
| 544 |
- @echo "Cleaning up." |
| 545 |
---- a/src/spacingFile/Makefile |
| 546 |
-+++ b/src/spacingFile/Makefile |
| 547 |
-@@ -37,7 +37,7 @@ |
| 548 |
- |
| 549 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 550 |
- @echo " * compiling" $(*F).cpp |
| 551 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(DFLAGS) $(INCLUDES) |
| 552 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 553 |
- |
| 554 |
- clean: |
| 555 |
- @echo "Cleaning up." |
| 556 |
---- a/src/split/Makefile |
| 557 |
-+++ b/src/split/Makefile |
| 558 |
-@@ -25,7 +25,7 @@ |
| 559 |
- |
| 560 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 561 |
- @echo " * compiling" $(*F).cpp |
| 562 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 563 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 564 |
- |
| 565 |
- clean: |
| 566 |
- @echo "Cleaning up." |
| 567 |
---- a/src/subtractFile/Makefile |
| 568 |
-+++ b/src/subtractFile/Makefile |
| 569 |
-@@ -40,7 +40,7 @@ |
| 570 |
- |
| 571 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 572 |
- @echo " * compiling" $(*F).cpp |
| 573 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) |
| 574 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 575 |
- |
| 576 |
- clean: |
| 577 |
- @echo "Cleaning up." |
| 578 |
---- a/src/tagBam/Makefile |
| 579 |
-+++ b/src/tagBam/Makefile |
| 580 |
-@@ -28,7 +28,7 @@ |
| 581 |
- |
| 582 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 583 |
- @echo " * compiling" $(*F).cpp |
| 584 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 585 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 586 |
- |
| 587 |
- clean: |
| 588 |
- @echo "Cleaning up." |
| 589 |
---- a/src/unionBedGraphs/Makefile |
| 590 |
-+++ b/src/unionBedGraphs/Makefile |
| 591 |
-@@ -27,7 +27,7 @@ |
| 592 |
- |
| 593 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 594 |
- @echo " * compiling" $(*F).cpp |
| 595 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 596 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 597 |
- |
| 598 |
- clean: |
| 599 |
- @echo "Cleaning up." |
| 600 |
---- a/src/utils/BamTools/Makefile |
| 601 |
-+++ b/src/utils/BamTools/Makefile |
| 602 |
-@@ -56,12 +56,12 @@ |
| 603 |
- |
| 604 |
- $(LIBRARY): $(OBJECTS) |
| 605 |
- @echo " * linking $(LIBRARY)" |
| 606 |
-- ar cr $@ $^ |
| 607 |
-+ $(AR) cr $@ $^ |
| 608 |
- -ranlib $@ |
| 609 |
- |
| 610 |
- $(OBJECTS): $(SOURCES) |
| 611 |
- @echo " * compiling" $(*F).cpp |
| 612 |
-- @$(CXX) -c $(*D)/$(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o |
| 613 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -o $(*D)/$(*F).o -c $(*D)/$(*F).cpp |
| 614 |
- |
| 615 |
- .PHONY: api |
| 616 |
- api: |
| 617 |
---- a/src/utils/BamTools-Ancillary/Makefile |
| 618 |
-+++ b/src/utils/BamTools-Ancillary/Makefile |
| 619 |
-@@ -21,7 +21,7 @@ |
| 620 |
- |
| 621 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 622 |
- @echo " * compiling" $(*F).cpp |
| 623 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib |
| 624 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp |
| 625 |
- |
| 626 |
- clean: |
| 627 |
- @echo "Cleaning up." |
| 628 |
---- a/src/utils/bedFile/Makefile |
| 629 |
-+++ b/src/utils/bedFile/Makefile |
| 630 |
-@@ -20,7 +20,7 @@ |
| 631 |
- |
| 632 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 633 |
- @echo " * compiling" $(*F).cpp |
| 634 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 635 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 636 |
- |
| 637 |
- $(EXT_OBJECTS): |
| 638 |
- @$(MAKE) --no-print-directory -C -W $(INCLUDES) |
| 639 |
---- a/src/utils/bedFilePE/Makefile |
| 640 |
-+++ b/src/utils/bedFilePE/Makefile |
| 641 |
-@@ -17,7 +17,7 @@ |
| 642 |
- |
| 643 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 644 |
- @echo " * compiling" $(*F).cpp |
| 645 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 646 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 647 |
- |
| 648 |
- $(EXT_OBJECTS): |
| 649 |
- @$(MAKE) --no-print-directory -C $(INCLUDES) |
| 650 |
---- a/src/utils/bedGraphFile/Makefile |
| 651 |
-+++ b/src/utils/bedGraphFile/Makefile |
| 652 |
-@@ -19,7 +19,7 @@ |
| 653 |
- |
| 654 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 655 |
- @echo " * compiling" $(*F).cpp |
| 656 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 657 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 658 |
- |
| 659 |
- $(EXT_OBJECTS): |
| 660 |
- @$(MAKE) --no-print-directory -C -W $(INCLUDES) |
| 661 |
---- a/src/utils/BinTree/Makefile |
| 662 |
-+++ b/src/utils/BinTree/Makefile |
| 663 |
-@@ -28,7 +28,7 @@ |
| 664 |
- |
| 665 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 666 |
- @echo " * compiling" $(*F).cpp |
| 667 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 668 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 669 |
- |
| 670 |
- $(EXT_OBJECTS): |
| 671 |
- @$(MAKE) --no-print-directory -C $(INCLUDES) |
| 672 |
---- a/src/utils/BlockedIntervals/Makefile |
| 673 |
-+++ b/src/utils/BlockedIntervals/Makefile |
| 674 |
-@@ -23,7 +23,7 @@ |
| 675 |
- |
| 676 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 677 |
- @echo " * compiling" $(*F).cpp |
| 678 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib |
| 679 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -L$(BT_ROOT)/lib -c -o $@ $(*F).cpp |
| 680 |
- |
| 681 |
- $(EXT_OBJECTS): |
| 682 |
- @$(MAKE) --no-print-directory -C $(INCLUDES) |
| 683 |
---- a/src/utils/chromsweep/Makefile |
| 684 |
-+++ b/src/utils/chromsweep/Makefile |
| 685 |
-@@ -20,7 +20,7 @@ |
| 686 |
- |
| 687 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 688 |
- @echo " * compiling" $(*F).cpp |
| 689 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 690 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 691 |
- |
| 692 |
- $(EXT_OBJECTS): |
| 693 |
- @$(MAKE) --no-print-directory -C $(INCLUDES) |
| 694 |
---- a/src/utils/Contexts/Makefile |
| 695 |
-+++ b/src/utils/Contexts/Makefile |
| 696 |
-@@ -36,7 +36,7 @@ |
| 697 |
- |
| 698 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 699 |
- @echo " * compiling" $(*F).cpp |
| 700 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 701 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 702 |
- |
| 703 |
- clean: |
| 704 |
- @echo "Cleaning up." |
| 705 |
---- a/src/utils/driver/Makefile |
| 706 |
-+++ b/src/utils/driver/Makefile |
| 707 |
-@@ -85,7 +85,7 @@ |
| 708 |
- |
| 709 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 710 |
- @echo " * compiling" $(*F).cpp |
| 711 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(DFLAGS) $(INCLUDES) |
| 712 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 713 |
- |
| 714 |
- clean: |
| 715 |
- @echo "Cleaning up." |
| 716 |
---- a/src/utils/Fasta/Makefile |
| 717 |
-+++ b/src/utils/Fasta/Makefile |
| 718 |
-@@ -19,7 +19,7 @@ |
| 719 |
- |
| 720 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 721 |
- @echo " * compiling" $(*F).cpp |
| 722 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) |
| 723 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 724 |
- |
| 725 |
- clean: |
| 726 |
- @echo "Cleaning up." |
| 727 |
---- a/src/utils/FileRecordTools/FileReaders/Makefile |
| 728 |
-+++ b/src/utils/FileRecordTools/FileReaders/Makefile |
| 729 |
-@@ -32,7 +32,7 @@ |
| 730 |
- |
| 731 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 732 |
- @echo " * compiling" $(*F).cpp |
| 733 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 734 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 735 |
- |
| 736 |
- clean: |
| 737 |
- @echo "Cleaning up." |
| 738 |
---- a/src/utils/FileRecordTools/FileReaders/Makefile~ |
| 739 |
-+++ b/src/utils/FileRecordTools/FileReaders/Makefile~ |
| 740 |
-@@ -31,7 +31,7 @@ |
| 741 |
- |
| 742 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 743 |
- @echo " * compiling" $(*F).cpp |
| 744 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 745 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 746 |
- |
| 747 |
- clean: |
| 748 |
- @echo "Cleaning up." |
| 749 |
---- a/src/utils/FileRecordTools/Makefile |
| 750 |
-+++ b/src/utils/FileRecordTools/Makefile |
| 751 |
-@@ -34,9 +34,9 @@ |
| 752 |
- |
| 753 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 754 |
- @echo " * compiling FileRecordMgr.cpp" |
| 755 |
-- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 756 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp |
| 757 |
- @echo " * compiling FileRecordMergeMgr.cpp" |
| 758 |
-- @$(CXX) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 759 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/FileRecordMergeMgr.o FileRecordMergeMgr.cpp |
| 760 |
- |
| 761 |
- |
| 762 |
- |
| 763 |
---- a/src/utils/FileRecordTools/Records/Makefile |
| 764 |
-+++ b/src/utils/FileRecordTools/Records/Makefile |
| 765 |
-@@ -37,7 +37,7 @@ |
| 766 |
- |
| 767 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 768 |
- @echo " * compiling" $(*F).cpp |
| 769 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 770 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 771 |
- |
| 772 |
- clean: |
| 773 |
- @echo "Cleaning up." |
| 774 |
---- a/src/utils/fileType/Makefile |
| 775 |
-+++ b/src/utils/fileType/Makefile |
| 776 |
-@@ -22,7 +22,7 @@ |
| 777 |
- |
| 778 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 779 |
- @echo " * compiling" $(*F).cpp |
| 780 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 781 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 782 |
- |
| 783 |
- clean: |
| 784 |
- @echo "Cleaning up." |
| 785 |
---- a/src/utils/general/Makefile |
| 786 |
-+++ b/src/utils/general/Makefile |
| 787 |
-@@ -21,7 +21,7 @@ |
| 788 |
- |
| 789 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 790 |
- @echo " * compiling" $(*F).cpp |
| 791 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 792 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 793 |
- |
| 794 |
- clean: |
| 795 |
- @echo "Cleaning up." |
| 796 |
---- a/src/utils/GenomeFile/Makefile |
| 797 |
-+++ b/src/utils/GenomeFile/Makefile |
| 798 |
-@@ -20,9 +20,9 @@ |
| 799 |
- |
| 800 |
- $(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS) |
| 801 |
- @echo " * compiling GenomeFile.cpp" |
| 802 |
-- @$(CXX) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 803 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/GenomeFile.o GenomeFile.cpp |
| 804 |
- @echo " * compiling NewGenomeFile.cpp" |
| 805 |
-- @$(CXX) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 806 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/NewGenomeFile.o NewGenomeFile.cpp |
| 807 |
- |
| 808 |
- #$(EXT_OBJECTS): |
| 809 |
- # @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/ |
| 810 |
---- a/src/utils/gzstream/Makefile |
| 811 |
-+++ b/src/utils/gzstream/Makefile |
| 812 |
-@@ -38,7 +38,7 @@ |
| 813 |
- UTILITIES_DIR = ../../utils/ |
| 814 |
- |
| 815 |
- ${OBJ_DIR}/gzstream.o : gzstream.C gzstream.h |
| 816 |
-- $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/gzstream.o gzstream.C $(INCLUDES) |
| 817 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $(OBJ_DIR)/gzstream.o gzstream.C |
| 818 |
- |
| 819 |
- clean: |
| 820 |
- @echo "Cleaning up." |
| 821 |
---- a/src/utils/KeyListOps/Makefile |
| 822 |
-+++ b/src/utils/KeyListOps/Makefile |
| 823 |
-@@ -31,7 +31,7 @@ |
| 824 |
- |
| 825 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 826 |
- @echo " * compiling" $(*F).cpp |
| 827 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 828 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 829 |
- |
| 830 |
- |
| 831 |
- $(EXT_OBJECTS): |
| 832 |
---- a/src/utils/NewChromsweep/Makefile |
| 833 |
-+++ b/src/utils/NewChromsweep/Makefile |
| 834 |
-@@ -34,7 +34,7 @@ |
| 835 |
- |
| 836 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 837 |
- @echo " * compiling" $(*F).cpp |
| 838 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 839 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 840 |
- |
| 841 |
- clean: |
| 842 |
- @echo "Cleaning up." |
| 843 |
---- a/src/utils/RecordOutputMgr/Makefile |
| 844 |
-+++ b/src/utils/RecordOutputMgr/Makefile |
| 845 |
-@@ -29,7 +29,7 @@ |
| 846 |
- |
| 847 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 848 |
- @echo " * compiling" $(*F).cpp |
| 849 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 850 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 851 |
- |
| 852 |
- $(EXT_OBJECTS): |
| 853 |
- @$(MAKE) --no-print-directory -C $(INCLUDES) |
| 854 |
---- a/src/utils/sequenceUtilities/Makefile |
| 855 |
-+++ b/src/utils/sequenceUtilities/Makefile |
| 856 |
-@@ -17,7 +17,7 @@ |
| 857 |
- |
| 858 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 859 |
- @echo " * compiling" $(*F).cpp |
| 860 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 861 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 862 |
- |
| 863 |
- $(EXT_OBJECTS): |
| 864 |
- @$(MAKE) --no-print-directory -C $(INCLUDES) |
| 865 |
---- a/src/utils/tabFile/Makefile |
| 866 |
-+++ b/src/utils/tabFile/Makefile |
| 867 |
-@@ -19,7 +19,7 @@ |
| 868 |
- |
| 869 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 870 |
- @echo " * compiling" $(*F).cpp |
| 871 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 872 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 873 |
- |
| 874 |
- $(EXT_OBJECTS): |
| 875 |
- @$(MAKE) --no-print-directory -C -W $(INCLUDES) |
| 876 |
---- a/src/utils/ToolBase/Makefile |
| 877 |
-+++ b/src/utils/ToolBase/Makefile |
| 878 |
-@@ -30,7 +30,7 @@ |
| 879 |
- |
| 880 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 881 |
- @echo " * compiling" $(*F).cpp |
| 882 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES) |
| 883 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 884 |
- |
| 885 |
- $(EXT_OBJECTS): |
| 886 |
- @$(MAKE) --no-print-directory -C $(INCLUDES) |
| 887 |
---- a/src/utils/VectorOps/Makefile |
| 888 |
-+++ b/src/utils/VectorOps/Makefile |
| 889 |
-@@ -11,7 +11,7 @@ |
| 890 |
- |
| 891 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 892 |
- @echo " * compiling" $(*F).cpp |
| 893 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 894 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 895 |
- |
| 896 |
- clean: |
| 897 |
- @echo "Cleaning up." |
| 898 |
---- a/src/utils/version/Makefile |
| 899 |
-+++ b/src/utils/version/Makefile |
| 900 |
-@@ -20,7 +20,7 @@ |
| 901 |
- |
| 902 |
- $(BUILT_OBJECTS): $(SOURCES) $(HEADERS) |
| 903 |
- @echo " * compiling" $(*F).cpp |
| 904 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) |
| 905 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 906 |
- |
| 907 |
- clean: |
| 908 |
- @echo "Cleaning up." |
| 909 |
---- a/src/windowBed/Makefile |
| 910 |
-+++ b/src/windowBed/Makefile |
| 911 |
-@@ -27,7 +27,7 @@ |
| 912 |
- |
| 913 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 914 |
- @echo " * compiling" $(*F).cpp |
| 915 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 916 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 917 |
- |
| 918 |
- clean: |
| 919 |
- @echo "Cleaning up." |
| 920 |
---- a/src/windowMaker/Makefile |
| 921 |
-+++ b/src/windowMaker/Makefile |
| 922 |
-@@ -26,7 +26,7 @@ |
| 923 |
- |
| 924 |
- $(BUILT_OBJECTS): $(SOURCES) |
| 925 |
- @echo " * compiling" $(*F).cpp |
| 926 |
-- @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) |
| 927 |
-+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) -c -o $@ $(*F).cpp |
| 928 |
- |
| 929 |
- $(EXT_OBJECTS): |
| 930 |
- @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/ |
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