@@ -1,4 +1,4 @@

-BUILT_RCPP_VERSION = package_version("0.12.5")

+BUILT_RCPP_VERSION = package_version("0.12.7")

 .onLoad <-

     function(libname, pkgname) {

@@ -19,18 +19,19 @@ PWIZOBJECTS=\

 ./boost/regex/src/w32_regex_traits.o \

 ./boost/iostreams/src/zlib.o \

 ./boost/iostreams/src/file_descriptor.o \

+./boost/thread/win32/tss_pe.o \

+./boost/thread/win32/tss_dll.o \

+./boost/thread/win32/thread.o \

 ./boost/filesystem/src/operations.o \

 ./boost/filesystem/src/path.o \

 ./boost/filesystem/src/path_traits.o \

-./boost/filesystem/src/utf8_codecvt_facet.o \

 ./boost/filesystem/src/windows_file_codecvt.o \

 ./boost/filesystem/src/codecvt_error_category.o \

+./boost/filesystem/src/utf8_codecvt_facet.o \

+./boost/chrono/src/chrono.o \

 ./boost/chrono/src/process_cpu_clocks.o \

 ./boost/chrono/src/thread_clock.o \

-./boost/chrono/src/chrono.o \

-./boost/thread/win32/tss_pe.o \

-./boost/thread/win32/thread.o \

-./boost_aux/boost/nowide/iostream.o \

+./pwiz/data/msdata/Version.o \

 ./pwiz/data/common/MemoryIndex.o \

 ./pwiz/data/common/CVTranslator.o \

 ./pwiz/data/common/cv.o \

@@ -38,7 +39,6 @@ PWIZOBJECTS=\

 ./pwiz/data/common/BinaryIndexStream.o \

 ./pwiz/data/common/diff_std.o \

 ./pwiz/data/common/Unimod.o \

-./pwiz/data/msdata/Version.o \

 ./pwiz/data/msdata/SpectrumList_MGF.o \

 ./pwiz/data/msdata/DefaultReaderList.o \

 ./pwiz/data/msdata/ChromatogramList_mzML.o \

@@ -59,14 +59,14 @@ PWIZOBJECTS=\

 ./pwiz/data/msdata/SpectrumList_BTDX.o \

 ./pwiz/data/msdata/SpectrumInfo.o \

 ./pwiz/data/msdata/RAMPAdapter.o \

+./pwiz/data/msdata/ramp/wglob.o \

 ./pwiz/data/msdata/LegacyAdapter.o \

 ./pwiz/data/msdata/SpectrumIterator.o \

 ./pwiz/data/msdata/MSDataFile.o \

 ./pwiz/data/msdata/MSNumpress.o \

 ./pwiz/data/msdata/SpectrumListCache.o \

-./pwiz/data/msdata/SpectrumWorkerThreads.o \

 ./pwiz/data/msdata/Index_mzML.o \

-./pwiz/data/msdata/ramp/wglob.o \

+./pwiz/data/msdata/SpectrumWorkerThreads.o \

 ./pwiz/data/identdata/IdentDataFile.o \

 ./pwiz/data/identdata/IdentData.o \

 ./pwiz/data/identdata/DefaultReaderList.o \

@@ -75,13 +75,14 @@ PWIZOBJECTS=\

 ./pwiz/data/identdata/Serializer_pepXML.o \

 ./pwiz/data/identdata/Serializer_mzid.o \

 ./pwiz/data/identdata/IO.o \

-./pwiz/data/identdata/Version.o \

 ./pwiz/data/identdata/References.o \

 ./pwiz/data/identdata/MascotReader.o \

 ./pwiz/data/proteome/Modification.o \

 ./pwiz/data/proteome/Digestion.o \

 ./pwiz/data/proteome/Peptide.o \

 ./pwiz/data/proteome/AminoAcid.o \

+./pwiz/utility/minimxml/XMLWriter.o \

+./pwiz/utility/minimxml/SAXParser.o \

 ./pwiz/utility/chemistry/Chemistry.o \

 ./pwiz/utility/chemistry/ChemistryData.o \

 ./pwiz/utility/chemistry/MZTolerance.o \

@@ -94,25 +95,26 @@ PWIZOBJECTS=\

 ./pwiz/utility/misc/random_access_compressed_ifstream.o \

 ./pwiz/utility/misc/SHA1.o \

 ./pwiz/utility/misc/SHA1Calculator.o \

-./pwiz/utility/minimxml/XMLWriter.o \

-./pwiz/utility/minimxml/SAXParser.o \

+./pwiz/utility/misc/sha1calc.o \

 ./random_access_gzFile.o 

-#./boost/thread/win32/tss_dll.o \

 MZROBJECTS=cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o RcppExports.o

-OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) rampR.o R_init_mzR.o

+OBJECTS=$(MZROBJECTS) $(PWIZOBJECTS) rampR.o R_init_mzR.o

 PWIZ_CPPFLAGS=-I./boost_aux/ -I./boost -I. -DHAVE_PWIZ_MZML_LIB  -DWITHOUT_MZ5 -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB

-ZLIB_CFLAGS+=$(shell echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'|\

-    "${R_HOME}/bin/R" --vanilla --slave)

+#ZLIB_CFLAGS=$(shell echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'|\

+#    "${R_HOME}/bin/R" --vanilla --slave)

+#ZLIB_CFLAGS="-Id:\local330\include"

+ZLIB_LDFLAGS="-lz"

+	

 ## Use the R_HOME indirection to support installations of multiple R version

-PKG_CPPFLAGS=-D_LARGEFILE_SOURCE $(ZLIB_CFLAGS) $(PWIZ_CPPFLAGS)  # last include only for cross-compiling

+PKG_CPPFLAGS=$(ZLIB_CFLAGS) -D_LARGEFILE_SOURCE $(PWIZ_CPPFLAGS)  # last include only for cross-compiling

-PKG_CFLAGS=-D_LARGEFILE_SOURCE -I./win/$(R_ARCH) -fgnu89-inline

+PKG_CFLAGS=$(ZLIB_CFLAGS) -D_LARGEFILE_SOURCE -I./win/$(R_ARCH) -fgnu89-inline

 ## Faster Linker on BioC build farm:

@@ -124,11 +126,8 @@ else

 	LD_ULDAR="-Wl,--dynamic-linker=$(ULDAR)/ld.exe"

 endif

-PKG_LIBS = $(LD_ULDAR) $(shell $(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()" ) $(PWIZ_LDFLAGS) -L./win/$(R_ARCH) -lws2_32 -lnetcdf

-

-PKG_LIBS+=$(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_shared")' |\

-    "${R_HOME}/bin/R" --vanilla --slave)

-

+#PKG_LIBS = $(LD_ULDAR) $(shell "${R_HOME}/bin/${R_ARCH_BIN}/Rscript.exe" -e "zlibbioc::pkgconfig(\"PKG_LIBS_shared\")") $(PWIZ_LDFLAGS) -lws2_32 -lnetcdf

+PKG_LIBS=$(PWIZ_LDFLAGS) -lws2_32 -lnetcdf -lz

 all: clean $(SHLIB)

@@ -140,26 +139,3 @@ all: clean $(SHLIB)

 clean:

 	rm -f $(OBJECTS)

-

-## As an alternative, one can also add this code in a file 'configure'

-##

-##    PKG_LIBS=`${R_HOME}/bin/Rscript -e "Rcpp:::LdFlags()"`

-##

-##    sed -e "s|@PKG_LIBS@|${PKG_LIBS}|" \

-##        src/Makevars.in > src/Makevars

-##

-## which together with the following file 'src/Makevars.in'

-##

-##    PKG_LIBS = @PKG_LIBS@

-##

-## can be used to create src/Makevars dynamically. This scheme is more

-## powerful and can be expanded to also check for and link with other

-## libraries.  It should be complemented by a file 'cleanup'

-##

-##    rm src/Makevars

-##

-## which removes the autogenerated file src/Makevars.

-##

-## Of course, autoconf can also be used to write configure files. This is

-## done by a number of packages, but recommended only for more advanced users

-## comfortable with autoconf and its related tools.