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  • Committer: Package Import Robot
  • Author(s): Thorsten Alteholz, Thorsten Alteholz, Andreas Tille
  • Date: 2014-02-02 22:51:35 UTC
  • mfrom: (7.1.1 sid)
  • Revision ID: package-import@ubuntu.com-20140202225135-nesemzj59jjgogh0
Tags: 4.0-1
http://bugs.debian.org/735798
[ Thorsten Alteholz ]
* New upstream version 
* debian/rules: add boost dir in auto_configure (Closes: #735798)

[ Andreas Tille ]
* cme fix dpkg-control
* debian/patches/{make.patch,spelling.patch}: applied upstream (thus removed)

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Lines of Context:
src/mira/Makefile.in
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        $(srcdir)/Makefile.am $(srcdir)/Makefile.in TODO \
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        parameters_flexer.cc
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ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
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am__aclocal_m4_deps = $(top_srcdir)/config/m4/ax_boost_base.m4 \
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        $(top_srcdir)/config/m4/ax_boost_filesystem.m4 \
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        $(top_srcdir)/config/m4/ax_boost_iostreams.m4 \
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        $(top_srcdir)/config/m4/ax_boost_regex.m4 \
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        $(top_srcdir)/config/m4/ax_boost_system.m4 \
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        $(top_srcdir)/config/m4/ax_boost_thread.m4 \
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        $(top_srcdir)/config/m4/ax_check_zlib.m4 \
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        $(top_srcdir)/config/m4/ax_cxx_have_std.m4 \
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        $(top_srcdir)/config/m4/ax_cxx_have_stl.m4 \
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        $(top_srcdir)/config/m4/ax_cxx_namespaces.m4 \
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        $(top_srcdir)/config/m4/ax_lib_expat.m4 \
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        $(top_srcdir)/config/m4/libtool.m4 \
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        $(top_srcdir)/config/m4/ltoptions.m4 \
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        $(top_srcdir)/config/m4/ltsugar.m4 \
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        $(top_srcdir)/config/m4/ltversion.m4 \
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        $(top_srcdir)/config/m4/lt~obsolete.m4 \
 
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am__aclocal_m4_deps = $(top_srcdir)/m4/ax_boost_base.m4 \
 
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        $(top_srcdir)/m4/ax_boost_filesystem.m4 \
 
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        $(top_srcdir)/m4/ax_boost_iostreams.m4 \
 
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        $(top_srcdir)/m4/ax_boost_regex.m4 \
 
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        $(top_srcdir)/m4/ax_boost_system.m4 \
 
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        $(top_srcdir)/m4/ax_boost_thread.m4 \
 
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        $(top_srcdir)/m4/ax_check_zlib.m4 \
 
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        $(top_srcdir)/m4/ax_cxx_have_std.m4 \
 
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        $(top_srcdir)/m4/ax_cxx_have_stl.m4 \
 
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        $(top_srcdir)/m4/ax_cxx_namespaces.m4 \
 
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        $(top_srcdir)/m4/ax_lib_expat.m4 $(top_srcdir)/m4/libtool.m4 \
 
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        $(top_srcdir)/m4/ltoptions.m4 $(top_srcdir)/m4/ltsugar.m4 \
 
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        $(top_srcdir)/m4/ltversion.m4 $(top_srcdir)/m4/lt~obsolete.m4 \
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        $(top_srcdir)/configure.ac
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am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
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        $(ACLOCAL_M4)
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libmira_a_AR = $(AR) $(ARFLAGS)
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libmira_a_LIBADD =
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am__objects_1 =
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am_libmira_a_OBJECTS = $(am__objects_1) preventinitfiasco.$(OBJEXT) \
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        sam_collect.$(OBJEXT) read.$(OBJEXT) parameters.$(OBJEXT) \
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        pcrcontainer.$(OBJEXT) ads.$(OBJEXT) adsfacts.$(OBJEXT) \
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        align.$(OBJEXT) assembly_output.$(OBJEXT) \
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        assembly_info.$(OBJEXT) contig_analysis.$(OBJEXT) \
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        contig_consensus.$(OBJEXT) contig_covanalysis.$(OBJEXT) \
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        contig_edit.$(OBJEXT) contig_featureinfo.$(OBJEXT) \
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        contig_pairconsistency.$(OBJEXT) contig_output.$(OBJEXT) \
 
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am_libmira_a_OBJECTS = $(am__objects_1) assembly.$(OBJEXT) \
 
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        contig.$(OBJEXT) read.$(OBJEXT) contig_analysis.$(OBJEXT) \
 
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        ads.$(OBJEXT) skim.$(OBJEXT) adsfacts.$(OBJEXT) \
 
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        align.$(OBJEXT) assembly_info.$(OBJEXT) assembly_io.$(OBJEXT) \
 
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        assembly_misc.$(OBJEXT) assembly_output.$(OBJEXT) \
 
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        assembly_reduceskimhits.$(OBJEXT) assembly_swalign.$(OBJEXT) \
 
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        bloomfilter.$(OBJEXT) contig_consensus.$(OBJEXT) \
 
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        contig_covanalysis.$(OBJEXT) contig_edit.$(OBJEXT) \
 
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        contig_featureinfo.$(OBJEXT) contig_output.$(OBJEXT) \
 
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        contig_pairconsistency.$(OBJEXT) dataprocessing.$(OBJEXT) \
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        dynamic.$(OBJEXT) gbf_parse.$(OBJEXT) gff_parse.$(OBJEXT) \
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        gff_save.$(OBJEXT) parameters_flexer.$(OBJEXT) \
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        maf_parse.$(OBJEXT) multitag.$(OBJEXT) readgrouplib.$(OBJEXT) \
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        contig.$(OBJEXT) readpool.$(OBJEXT) assembly.$(OBJEXT) \
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        bloomfilter.$(OBJEXT) ppathfinder.$(OBJEXT) skim.$(OBJEXT) \
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        hashstats.$(OBJEXT) assembly_io.$(OBJEXT) \
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        assembly_reduceskimhits.$(OBJEXT) assembly_swalign.$(OBJEXT) \
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        assembly_misc.$(OBJEXT) dataprocessing.$(OBJEXT) \
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        manifest.$(OBJEXT) scaffolder.$(OBJEXT) seqtohash.$(OBJEXT) \
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        skim_farc.$(OBJEXT) skim_lowbph.$(OBJEXT)
 
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        gff_save.$(OBJEXT) hashstats.$(OBJEXT) maf_parse.$(OBJEXT) \
 
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        manifest.$(OBJEXT) multitag.$(OBJEXT) \
 
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        parameters_flexer.$(OBJEXT) parameters.$(OBJEXT) \
 
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        pcrcontainer.$(OBJEXT) ppathfinder.$(OBJEXT) \
 
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        preventinitfiasco.$(OBJEXT) readgrouplib.$(OBJEXT) \
 
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        readpool.$(OBJEXT) sam_collect.$(OBJEXT) scaffolder.$(OBJEXT) \
 
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        seqtohash.$(OBJEXT) skim_farc.$(OBJEXT) skim_lowbph.$(OBJEXT) \
 
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        warnings.$(OBJEXT)
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nodist_libmira_a_OBJECTS = $(am__objects_1)
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libmira_a_OBJECTS = $(am_libmira_a_OBJECTS) \
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        $(nodist_libmira_a_OBJECTS)
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BOOST_REGEX_LIB = @BOOST_REGEX_LIB@
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BOOST_SYSTEM_LIB = @BOOST_SYSTEM_LIB@
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BOOST_THREAD_LIB = @BOOST_THREAD_LIB@
 
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BUNDLETARGET = @BUNDLETARGET@
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CC = @CC@
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CCDEPMODE = @CCDEPMODE@
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CFLAGS = @CFLAGS@
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nodist_libmira_a_SOURCES = $(libmira_a_XXDSRC:.xxd=.xxd.H)
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dist_pkgdata_DATA = demoparam.prm
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# put read and contig in front: with make -j .... they'll get made first
 
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# put assembly, read, contig, etc. in front: with make -j .... they'll get made first
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#  and won't block the rest.
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libmira_a_SOURCES = \
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        $(libmira_a_XXDSRC) \
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        preventinitfiasco.C\
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        sam_collect.C\
 
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        assembly.C\
 
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        contig.C\
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        read.C\
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        parameters.C \
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        pcrcontainer.C \
 
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        contig_analysis.C\
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        ads.C\
 
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        skim.C\
 
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        \
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        adsfacts.C\
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        align.C\
 
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        assembly_info.C\
 
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        assembly_io.C\
 
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        assembly_misc.C\
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        assembly_output.C\
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        assembly_info.C\
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        contig_analysis.C\
 
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        assembly_reduceskimhits.C\
 
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        assembly_swalign.C\
 
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        bloomfilter.C\
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        contig_consensus.C\
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        contig_covanalysis.C\
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        contig_edit.C\
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        contig_featureinfo.C\
 
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        contig_output.C\
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        contig_pairconsistency.C\
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        contig_output.C\
 
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        dataprocessing.C\
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        dynamic.C\
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        gbf_parse.C\
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        gff_parse.C\
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        gff_save.C\
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        parameters_flexer.ll\
 
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        hashstats.C\
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        maf_parse.C\
 
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        manifest.C\
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        multitag.C\
 
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        parameters_flexer.ll\
 
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        parameters.C \
 
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        pcrcontainer.C \
 
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        ppathfinder.C\
 
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        preventinitfiasco.C\
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        readgrouplib.C\
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        contig.C\
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        readpool.C\
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        assembly.C\
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        bloomfilter.C\
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        ppathfinder.C\
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        skim.C\
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        hashstats.C\
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        assembly_io.C\
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        assembly_reduceskimhits.C\
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        assembly_swalign.C\
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        assembly_misc.C\
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        dataprocessing.C\
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        manifest.C\
 
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        sam_collect.C\
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        scaffolder.C\
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        seqtohash.C\
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        skim_farc.C\
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        skim_lowbph.C
 
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        skim_lowbph.C\
 
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        warnings.C
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noinst_HEADERS = adsfacts.H\
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        ads.H\
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        stringcontainer.H\
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        structs.H\
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        timerestrict.H\
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        types_basic.H
 
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        types_basic.H\
 
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        warnings.H
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libmiraestass_a_SOURCES = estassembly.C
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all: $(BUILT_SOURCES)
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/skim.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/skim_farc.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/skim_lowbph.Po@am__quote@
 
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/warnings.Po@am__quote@
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.C.o:
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@am__fastdepCXX_TRUE@   $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<