[Genabel-commits] r743 - in branches/ProbABEL/autotools-integration/ProbABEL: . src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 23 13:44:32 CEST 2011
Author: lckarssen
Date: 2011-06-23 13:44:32 +0200 (Thu, 23 Jun 2011)
New Revision: 743
Modified:
branches/ProbABEL/autotools-integration/ProbABEL/
branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.am
branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.in
Log:
In the ProbABEL autotools integration branch:
- Added the ProbABEL tar.gz package is now in the ignore list.
- Adjusted Makefile.am to copy probabel_config.cfg during `make install`
Property changes on: branches/ProbABEL/autotools-integration/ProbABEL
___________________________________________________________________
Modified: svn:ignore
- .project
+ .project
autom4te.cache
ProbABEL-0.1-9e.tar.gz
Modified: branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.am
===================================================================
--- branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.am 2011-06-22 18:10:38 UTC (rev 742)
+++ branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.am 2011-06-23 11:44:32 UTC (rev 743)
@@ -7,9 +7,7 @@
## I tried :-).
REGFILES = data.h mematrix.h reg1.h usage.h main.cpp version.h mematri1.h
-COXBASE = chinv2 cholesky2 chsolve2 dmatrix
-COXSRC = $(COXBASE:=.c) coxfit2.c
-
+## Filevector files:
FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp \
fvlib/convert_util.cpp fvlib/FileVector.cpp fvlib/FilteredMatrix.cpp \
fvlib/frutil.cpp fvlib/Logger.cpp fvlib/RealHandlerWrapper.cpp \
@@ -20,8 +18,13 @@
fvlib/ReusableFileHandle.h fvlib/RealHandlerWrapper.h \
fvlib/FilteredMatrix.h
+## Extra files for pacoxph
+COXBASE = chinv2 cholesky2 chsolve2 dmatrix
+COXSRC = $(COXBASE:=.c) coxfit2.c
+
+
bin_PROGRAMS = palinear palogist
-#pacoxph
+#bin_PROGRAMS = pacoxph
palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
palinear_CXXFLAGS = -DLINEAR
@@ -33,14 +36,19 @@
# pacoxph_CXXFLAGS = -DCOXPH -I include
# pacoxph_CFLAGS = -DCOXPH -I include
+## Install these scripts in the bin directory as well:
dist_bin_SCRIPTS = probabel.pl extIDS.pl
+## Install the config file
+dist_sysconf_DATA = probabel_config.cfg
+
+
## Old Makefile rules
-# palinear: $(REGFILES)
-# $(CXX) $(CXXFLAGS) -DLINEAR main.cpp $(FVSRC) -o $@
+## palinear: $(REGFILES)
+## $(CXX) $(CXXFLAGS) -DLINEAR main.cpp $(FVSRC) -o $@
-# palogist: $(REGFILES)
-# $(CPP) $(CFLAGS) -DLOGISTIC main.cpp fvlib/*.cpp -o $(LOGREG)
+## palogist: $(REGFILES)
+## $(CPP) $(CFLAGS) -DLOGISTIC main.cpp fvlib/*.cpp -o $(LOGREG)
-# pacoxph: $(COXSRC) $(REGFILES)
-# $(CPP) $(CFLAGS) -DCOXPH $(COXSRC) main.cpp fvlib/*.cpp -o $(COXREG)
+## pacoxph: $(COXSRC) $(REGFILES)
+## $(CPP) $(CFLAGS) -DCOXPH $(COXSRC) main.cpp fvlib/*.cpp -o $(COXREG)
Modified: branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.in
===================================================================
--- branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.in 2011-06-22 18:10:38 UTC (rev 742)
+++ branches/ProbABEL/autotools-integration/ProbABEL/src/Makefile.in 2011-06-23 11:44:32 UTC (rev 743)
@@ -16,6 +16,7 @@
@SET_MAKE@
+
VPATH = @srcdir@
pkgdatadir = $(datadir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@
@@ -33,10 +34,11 @@
NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
-bin_PROGRAMS = palinear$(EXEEXT) palogist$(EXEEXT)
+bin_PROGRAMS = pacoxph$(EXEEXT)
subdir = src
-DIST_COMMON = $(dist_bin_SCRIPTS) $(srcdir)/Makefile.am \
- $(srcdir)/Makefile.in $(srcdir)/config.h.in
+DIST_COMMON = $(dist_bin_SCRIPTS) $(dist_sysconf_DATA) \
+ $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
+ $(srcdir)/config.h.in
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
@@ -45,39 +47,27 @@
CONFIG_HEADER = config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
-am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)"
+am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" \
+ "$(DESTDIR)$(sysconfdir)"
PROGRAMS = $(bin_PROGRAMS)
-am__objects_1 = palinear-main.$(OBJEXT)
-am__objects_2 = palinear-AbstractMatrix.$(OBJEXT) \
- palinear-CastUtils.$(OBJEXT) palinear-convert_util.$(OBJEXT) \
- palinear-FileVector.$(OBJEXT) \
- palinear-FilteredMatrix.$(OBJEXT) palinear-frutil.$(OBJEXT) \
- palinear-Logger.$(OBJEXT) \
- palinear-RealHandlerWrapper.$(OBJEXT) \
- palinear-ReusableFileHandle.$(OBJEXT) \
- palinear-Transposer.$(OBJEXT)
+am__objects_1 = pacoxph-main.$(OBJEXT)
+am__objects_2 = pacoxph-AbstractMatrix.$(OBJEXT) \
+ pacoxph-CastUtils.$(OBJEXT) pacoxph-convert_util.$(OBJEXT) \
+ pacoxph-FileVector.$(OBJEXT) pacoxph-FilteredMatrix.$(OBJEXT) \
+ pacoxph-frutil.$(OBJEXT) pacoxph-Logger.$(OBJEXT) \
+ pacoxph-RealHandlerWrapper.$(OBJEXT) \
+ pacoxph-ReusableFileHandle.$(OBJEXT) \
+ pacoxph-Transposer.$(OBJEXT)
am__objects_3 =
-am_palinear_OBJECTS = $(am__objects_1) $(am__objects_2) \
- $(am__objects_3)
-palinear_OBJECTS = $(am_palinear_OBJECTS)
-palinear_LDADD = $(LDADD)
-palinear_LINK = $(CXXLD) $(palinear_CXXFLAGS) $(CXXFLAGS) \
- $(AM_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_4 = palogist-main.$(OBJEXT)
-am__objects_5 = palogist-AbstractMatrix.$(OBJEXT) \
- palogist-CastUtils.$(OBJEXT) palogist-convert_util.$(OBJEXT) \
- palogist-FileVector.$(OBJEXT) \
- palogist-FilteredMatrix.$(OBJEXT) palogist-frutil.$(OBJEXT) \
- palogist-Logger.$(OBJEXT) \
- palogist-RealHandlerWrapper.$(OBJEXT) \
- palogist-ReusableFileHandle.$(OBJEXT) \
- palogist-Transposer.$(OBJEXT)
-am_palogist_OBJECTS = $(am__objects_4) $(am__objects_5) \
- $(am__objects_3)
-palogist_OBJECTS = $(am_palogist_OBJECTS)
-palogist_LDADD = $(LDADD)
-palogist_LINK = $(CXXLD) $(palogist_CXXFLAGS) $(CXXFLAGS) \
- $(AM_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_4 = pacoxph-chinv2.$(OBJEXT) pacoxph-cholesky2.$(OBJEXT) \
+ pacoxph-chsolve2.$(OBJEXT) pacoxph-dmatrix.$(OBJEXT)
+am__objects_5 = $(am__objects_4) pacoxph-coxfit2.$(OBJEXT)
+am_pacoxph_OBJECTS = $(am__objects_1) $(am__objects_2) \
+ $(am__objects_3) $(am__objects_5)
+pacoxph_OBJECTS = $(am_pacoxph_OBJECTS)
+pacoxph_LDADD = $(LDADD)
+pacoxph_LINK = $(CXXLD) $(pacoxph_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
+ $(LDFLAGS) -o $@
am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
am__vpath_adj = case $$p in \
$(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
@@ -104,17 +94,18 @@
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
am__mv = mv -f
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
CXXLD = $(CXX)
CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \
-o $@
-COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
-CCLD = $(CC)
-LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
-SOURCES = $(palinear_SOURCES) $(palogist_SOURCES)
-DIST_SOURCES = $(palinear_SOURCES) $(palogist_SOURCES)
+SOURCES = $(pacoxph_SOURCES)
+DIST_SOURCES = $(pacoxph_SOURCES)
+DATA = $(dist_sysconf_DATA)
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
@@ -214,8 +205,6 @@
AM_CFLAGS = -I include -O2
AM_LDFLAGS =
REGFILES = data.h mematrix.h reg1.h usage.h main.cpp version.h mematri1.h
-COXBASE = chinv2 cholesky2 chsolve2 dmatrix
-COXSRC = $(COXBASE:=.c) coxfit2.c
FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp \
fvlib/convert_util.cpp fvlib/FileVector.cpp fvlib/FilteredMatrix.cpp \
fvlib/frutil.cpp fvlib/Logger.cpp fvlib/RealHandlerWrapper.cpp \
@@ -227,21 +216,24 @@
fvlib/ReusableFileHandle.h fvlib/RealHandlerWrapper.h \
fvlib/FilteredMatrix.h
-#pacoxph
-palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
-palinear_CXXFLAGS = -DLINEAR
-palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
-palogist_CXXFLAGS = -DLOGISTIC
+COXBASE = chinv2 cholesky2 chsolve2 dmatrix
+COXSRC = $(COXBASE:=.c) coxfit2.c
-# pacoxph_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS) $(COXSRC)
-# pacoxph_CXXFLAGS = -DCOXPH -I include
-# pacoxph_CFLAGS = -DCOXPH -I include
+# palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
+# palinear_CXXFLAGS = -DLINEAR
+
+# palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
+# palogist_CXXFLAGS = -DLOGISTIC
+pacoxph_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS) $(COXSRC)
+pacoxph_CXXFLAGS = -DCOXPH -I include
+pacoxph_CFLAGS = -DCOXPH -I include
dist_bin_SCRIPTS = probabel.pl extIDS.pl
+dist_sysconf_DATA = probabel_config.cfg
all: config.h
$(MAKE) $(AM_MAKEFLAGS) all-am
.SUFFIXES:
-.SUFFIXES: .cpp .o .obj
+.SUFFIXES: .c .cpp .o .obj
$(srcdir)/Makefile.in: $(srcdir)/Makefile.am $(am__configure_deps)
@for dep in $?; do \
case '$(am__configure_deps)' in \
@@ -326,12 +318,9 @@
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
-palinear$(EXEEXT): $(palinear_OBJECTS) $(palinear_DEPENDENCIES)
- @rm -f palinear$(EXEEXT)
- $(palinear_LINK) $(palinear_OBJECTS) $(palinear_LDADD) $(LIBS)
-palogist$(EXEEXT): $(palogist_OBJECTS) $(palogist_DEPENDENCIES)
- @rm -f palogist$(EXEEXT)
- $(palogist_LINK) $(palogist_OBJECTS) $(palogist_LDADD) $(LIBS)
+pacoxph$(EXEEXT): $(pacoxph_OBJECTS) $(pacoxph_DEPENDENCIES)
+ @rm -f pacoxph$(EXEEXT)
+ $(pacoxph_LINK) $(pacoxph_OBJECTS) $(pacoxph_LDADD) $(LIBS)
install-dist_binSCRIPTS: $(dist_bin_SCRIPTS)
@$(NORMAL_INSTALL)
test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)"
@@ -373,351 +362,295 @@
distclean-compile:
-rm -f *.tab.c
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-AbstractMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-CastUtils.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-FileVector.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-FilteredMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-Logger.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-RealHandlerWrapper.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-ReusableFileHandle.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-Transposer.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-convert_util.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-frutil.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-main.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-AbstractMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-CastUtils.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-FileVector.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-FilteredMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-Logger.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-RealHandlerWrapper.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-ReusableFileHandle.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-Transposer.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-convert_util.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-frutil.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-main.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-AbstractMatrix.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-CastUtils.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-FileVector.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-FilteredMatrix.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-Logger.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-RealHandlerWrapper.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-ReusableFileHandle.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-Transposer.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-chinv2.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-cholesky2.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-chsolve2.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-convert_util.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-coxfit2.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-dmatrix.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-frutil.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-main.Po at am__quote@
-.cpp.o:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
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- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ $<
+.c.o:
+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(COMPILE) -c $<
-.cpp.obj:
- at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
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- at am__fastdepCXX_FALSE@ $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`
+.c.obj:
+ at am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
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-palinear-main.o: main.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-main.o -MD -MP -MF $(DEPDIR)/palinear-main.Tpo -c -o palinear-main.o `test -f 'main.cpp' || echo '$(srcdir)/'`main.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/palinear-main.Tpo $(DEPDIR)/palinear-main.Po
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+pacoxph-chinv2.o: chinv2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-chinv2.o -MD -MP -MF $(DEPDIR)/pacoxph-chinv2.Tpo -c -o pacoxph-chinv2.o `test -f 'chinv2.c' || echo '$(srcdir)/'`chinv2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-chinv2.Tpo $(DEPDIR)/pacoxph-chinv2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chinv2.c' object='pacoxph-chinv2.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-chinv2.o `test -f 'chinv2.c' || echo '$(srcdir)/'`chinv2.c
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+pacoxph-chinv2.obj: chinv2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-chinv2.obj -MD -MP -MF $(DEPDIR)/pacoxph-chinv2.Tpo -c -o pacoxph-chinv2.obj `if test -f 'chinv2.c'; then $(CYGPATH_W) 'chinv2.c'; else $(CYGPATH_W) '$(srcdir)/chinv2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-chinv2.Tpo $(DEPDIR)/pacoxph-chinv2.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-chinv2.obj `if test -f 'chinv2.c'; then $(CYGPATH_W) 'chinv2.c'; else $(CYGPATH_W) '$(srcdir)/chinv2.c'; fi`
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- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/palinear-AbstractMatrix.Tpo $(DEPDIR)/palinear-AbstractMatrix.Po
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+pacoxph-cholesky2.o: cholesky2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-cholesky2.o -MD -MP -MF $(DEPDIR)/pacoxph-cholesky2.Tpo -c -o pacoxph-cholesky2.o `test -f 'cholesky2.c' || echo '$(srcdir)/'`cholesky2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-cholesky2.Tpo $(DEPDIR)/pacoxph-cholesky2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cholesky2.c' object='pacoxph-cholesky2.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-cholesky2.o `test -f 'cholesky2.c' || echo '$(srcdir)/'`cholesky2.c
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+pacoxph-cholesky2.obj: cholesky2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-cholesky2.obj -MD -MP -MF $(DEPDIR)/pacoxph-cholesky2.Tpo -c -o pacoxph-cholesky2.obj `if test -f 'cholesky2.c'; then $(CYGPATH_W) 'cholesky2.c'; else $(CYGPATH_W) '$(srcdir)/cholesky2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-cholesky2.Tpo $(DEPDIR)/pacoxph-cholesky2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cholesky2.c' object='pacoxph-cholesky2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-cholesky2.obj `if test -f 'cholesky2.c'; then $(CYGPATH_W) 'cholesky2.c'; else $(CYGPATH_W) '$(srcdir)/cholesky2.c'; fi`
-palinear-CastUtils.o: fvlib/CastUtils.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-CastUtils.o -MD -MP -MF $(DEPDIR)/palinear-CastUtils.Tpo -c -o palinear-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo '$(srcdir)/'`fvlib/CastUtils.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/palinear-CastUtils.Tpo $(DEPDIR)/palinear-CastUtils.Po
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- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-CastUtils.o `test -f 'fvlib/CastUtils.cpp' || echo '$(srcdir)/'`fvlib/CastUtils.cpp
+pacoxph-chsolve2.o: chsolve2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-chsolve2.o -MD -MP -MF $(DEPDIR)/pacoxph-chsolve2.Tpo -c -o pacoxph-chsolve2.o `test -f 'chsolve2.c' || echo '$(srcdir)/'`chsolve2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-chsolve2.Tpo $(DEPDIR)/pacoxph-chsolve2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chsolve2.c' object='pacoxph-chsolve2.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-chsolve2.o `test -f 'chsolve2.c' || echo '$(srcdir)/'`chsolve2.c
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- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-CastUtils.obj -MD -MP -MF $(DEPDIR)/palinear-CastUtils.Tpo -c -o palinear-CastUtils.obj `if test -f 'fvlib/CastUtils.cpp'; then $(CYGPATH_W) 'fvlib/CastUtils.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/CastUtils.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/palinear-CastUtils.Tpo $(DEPDIR)/palinear-CastUtils.Po
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- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-CastUtils.obj `if test -f 'fvlib/CastUtils.cpp'; then $(CYGPATH_W) 'fvlib/CastUtils.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/CastUtils.cpp'; fi`
+pacoxph-chsolve2.obj: chsolve2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-chsolve2.obj -MD -MP -MF $(DEPDIR)/pacoxph-chsolve2.Tpo -c -o pacoxph-chsolve2.obj `if test -f 'chsolve2.c'; then $(CYGPATH_W) 'chsolve2.c'; else $(CYGPATH_W) '$(srcdir)/chsolve2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-chsolve2.Tpo $(DEPDIR)/pacoxph-chsolve2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chsolve2.c' object='pacoxph-chsolve2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-chsolve2.obj `if test -f 'chsolve2.c'; then $(CYGPATH_W) 'chsolve2.c'; else $(CYGPATH_W) '$(srcdir)/chsolve2.c'; fi`
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- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-convert_util.o -MD -MP -MF $(DEPDIR)/palinear-convert_util.Tpo -c -o palinear-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo '$(srcdir)/'`fvlib/convert_util.cpp
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- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-convert_util.o `test -f 'fvlib/convert_util.cpp' || echo '$(srcdir)/'`fvlib/convert_util.cpp
+pacoxph-dmatrix.o: dmatrix.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-dmatrix.o -MD -MP -MF $(DEPDIR)/pacoxph-dmatrix.Tpo -c -o pacoxph-dmatrix.o `test -f 'dmatrix.c' || echo '$(srcdir)/'`dmatrix.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-dmatrix.Tpo $(DEPDIR)/pacoxph-dmatrix.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dmatrix.c' object='pacoxph-dmatrix.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-dmatrix.o `test -f 'dmatrix.c' || echo '$(srcdir)/'`dmatrix.c
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- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-convert_util.obj -MD -MP -MF $(DEPDIR)/palinear-convert_util.Tpo -c -o palinear-convert_util.obj `if test -f 'fvlib/convert_util.cpp'; then $(CYGPATH_W) 'fvlib/convert_util.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/convert_util.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/palinear-convert_util.Tpo $(DEPDIR)/palinear-convert_util.Po
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+pacoxph-dmatrix.obj: dmatrix.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-dmatrix.obj -MD -MP -MF $(DEPDIR)/pacoxph-dmatrix.Tpo -c -o pacoxph-dmatrix.obj `if test -f 'dmatrix.c'; then $(CYGPATH_W) 'dmatrix.c'; else $(CYGPATH_W) '$(srcdir)/dmatrix.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-dmatrix.Tpo $(DEPDIR)/pacoxph-dmatrix.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dmatrix.c' object='pacoxph-dmatrix.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-dmatrix.obj `if test -f 'dmatrix.c'; then $(CYGPATH_W) 'dmatrix.c'; else $(CYGPATH_W) '$(srcdir)/dmatrix.c'; fi`
-palinear-FileVector.o: fvlib/FileVector.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-FileVector.o -MD -MP -MF $(DEPDIR)/palinear-FileVector.Tpo -c -o palinear-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo '$(srcdir)/'`fvlib/FileVector.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/palinear-FileVector.Tpo $(DEPDIR)/palinear-FileVector.Po
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- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-FileVector.o `test -f 'fvlib/FileVector.cpp' || echo '$(srcdir)/'`fvlib/FileVector.cpp
+pacoxph-coxfit2.o: coxfit2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-coxfit2.o -MD -MP -MF $(DEPDIR)/pacoxph-coxfit2.Tpo -c -o pacoxph-coxfit2.o `test -f 'coxfit2.c' || echo '$(srcdir)/'`coxfit2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-coxfit2.Tpo $(DEPDIR)/pacoxph-coxfit2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='coxfit2.c' object='pacoxph-coxfit2.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-coxfit2.o `test -f 'coxfit2.c' || echo '$(srcdir)/'`coxfit2.c
-palinear-FileVector.obj: fvlib/FileVector.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-FileVector.obj -MD -MP -MF $(DEPDIR)/palinear-FileVector.Tpo -c -o palinear-FileVector.obj `if test -f 'fvlib/FileVector.cpp'; then $(CYGPATH_W) 'fvlib/FileVector.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/FileVector.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/palinear-FileVector.Tpo $(DEPDIR)/palinear-FileVector.Po
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- at am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -c -o palinear-FileVector.obj `if test -f 'fvlib/FileVector.cpp'; then $(CYGPATH_W) 'fvlib/FileVector.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/FileVector.cpp'; fi`
+pacoxph-coxfit2.obj: coxfit2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -MT pacoxph-coxfit2.obj -MD -MP -MF $(DEPDIR)/pacoxph-coxfit2.Tpo -c -o pacoxph-coxfit2.obj `if test -f 'coxfit2.c'; then $(CYGPATH_W) 'coxfit2.c'; else $(CYGPATH_W) '$(srcdir)/coxfit2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/pacoxph-coxfit2.Tpo $(DEPDIR)/pacoxph-coxfit2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='coxfit2.c' object='pacoxph-coxfit2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(pacoxph_CFLAGS) $(CFLAGS) -c -o pacoxph-coxfit2.obj `if test -f 'coxfit2.c'; then $(CYGPATH_W) 'coxfit2.c'; else $(CYGPATH_W) '$(srcdir)/coxfit2.c'; fi`
-palinear-FilteredMatrix.o: fvlib/FilteredMatrix.cpp
- at am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-FilteredMatrix.o -MD -MP -MF $(DEPDIR)/palinear-FilteredMatrix.Tpo -c -o palinear-FilteredMatrix.o `test -f 'fvlib/FilteredMatrix.cpp' || echo '$(srcdir)/'`fvlib/FilteredMatrix.cpp
- at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/palinear-FilteredMatrix.Tpo $(DEPDIR)/palinear-FilteredMatrix.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='fvlib/FilteredMatrix.cpp' object='palinear-FilteredMatrix.o' libtool=no @AMDEPBACKSLASH@
+.cpp.o:
+ at am__fastdepCXX_TRUE@ $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ at am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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