Browse code

Fix compile errors by win_check()

uly55e5 authored on 24/01/2022 17:18:46
Showing6 changed files

... ...
@@ -39,7 +39,6 @@ Suggests:
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 VignetteBuilder: knitr
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 LinkingTo:
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     Rcpp,
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-    zlibbioc,
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     Rhdf5lib (>= 1.1.4)
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 RcppModules:
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     Pwiz,
... ...
@@ -38,6 +38,8 @@ PWIZOBJECTS=\
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 ./boost/filesystem/src/codecvt_error_category.o \
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 ./boost/thread/win32/thread.o \
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 ./boost_aux/boost/nowide/iostream.o \
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+./boost_aux/boost/nowide/filebuf.o \
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+./boost_aux/libs/nowide/src/cstdio.o \
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 ./pwiz/data/common/MemoryIndex.o \
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 ./pwiz/data/common/CVTranslator.o \
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 ./pwiz/data/common/cv.o \
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@@ -105,6 +107,6 @@ all: libpwiz.a
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 libpwiz.a: $(PWIZOBJECTS)
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 	ar -rc $@ $(PWIZOBJECTS)
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-	
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+
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 clean:
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-	rm -rf $(PWIZOBJECTS)
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\ No newline at end of file
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+	rm -rf $(PWIZOBJECTS)
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@@ -102,14 +102,21 @@ ARCH_OBJS=./boost/libs/filesystem/src/path_traits.o \
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 ./boost/libs/thread/src/win32/tss_pe.o \
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 ./boost/libs/thread/src/win32/tss_dll.o \
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 ./boost/libs/thread/src/win32/thread.o \
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-./boost_aux/libs/nowide/src/iostream.o
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+./boost_aux/libs/nowide/src/iostream.o \
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+./boost_aux/libs/nowide/src/cstdio.o \
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+./boost_aux/libs/nowide/src/filebuf.o
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 ARCH_CPPFLAGS=-fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB
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 ARCH_LIBS=-lws2_32 -lz
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-RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)  
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+RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)
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+ZLIB_CFLAGS=$(shell echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "${R_HOME}/bin/R" --vanilla --slave)
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+ZLIB_LIBS=$(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_shared")' | "${R_HOME}/bin/R" --vanilla --slave)
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 else
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 ARCH_OBJS=./boost/libs/thread/src/pthread/once.o \
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 ./boost/libs/thread/src/pthread/thread.o
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 RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)
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+ZLIB_CFLAGS=$(shell echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'|\
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+"${R_HOME}/bin/R" --vanilla --slave)
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+ZLIB_LIBS=$(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_shared")' | "${R_HOME}/bin/R" --vanilla --slave)
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 endif
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 MZROBJECTS= RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o
... ...
@@ -117,7 +124,7 @@ MZROBJECTS= RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o
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 OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) $(ARCH_OBJS)
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 ## Generate dependency files
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-#DEPFLAGS = -MT $@ -MMD -MP 
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+#DEPFLAGS = -MT $@ -MMD -MP
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 ##
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 ## R complains about assert(), hence -D_NODEBUG
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new file mode 100644
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@@ -0,0 +1,141 @@
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+PWIZOBJECTS=\
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+./boost/libs/system/src/error_code.o \
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+./boost/libs/regex/src/posix_api.o \
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+./boost/libs/regex/src/regex_debug.o \
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+./boost/libs/regex/src/regex.o \
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+./boost/libs/regex/src/wide_posix_api.o \
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+./boost/libs/regex/src/static_mutex.o \
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+./boost/libs/iostreams/src/zlib.o \
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+./boost/libs/iostreams/src/file_descriptor.o \
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+./boost/libs/filesystem/src/operations.o \
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+./boost/libs/filesystem/src/directory.o \
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+./boost/libs/filesystem/src/exception.o \
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+./boost/libs/filesystem/src/path.o \
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+./boost/libs/filesystem/src/unique_path.o \
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+./boost/libs/filesystem/src/utf8_codecvt_facet.o \
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+./boost/libs/chrono/src/chrono.o \
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+./boost/libs/chrono/src/process_cpu_clocks.o \
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+./boost/libs/chrono/src/thread_clock.o \
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+./pwiz/data/msdata/Version.o \
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+./pwiz/data/identdata/Version.o \
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+./pwiz/data/common/MemoryIndex.o \
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+./pwiz/data/common/CVTranslator.o \
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+./pwiz/data/common/cv.o \
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+./pwiz/data/common/ParamTypes.o \
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+./pwiz/data/common/BinaryIndexStream.o \
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+./pwiz/data/common/diff_std.o \
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+./pwiz/data/common/Unimod.o \
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+./pwiz/data/msdata/mz5/Configuration_mz5.o \
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+./pwiz/data/msdata/mz5/Connection_mz5.o \
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+./pwiz/data/msdata/mz5/Datastructures_mz5.o \
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+./pwiz/data/msdata/mz5/ReferenceRead_mz5.o \
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+./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o \
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+./pwiz/data/msdata/mz5/Translator_mz5.o \
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+./pwiz/data/msdata/DefaultReaderList.o \
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+./pwiz/data/msdata/ChromatogramList_mzML.o \
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+./pwiz/data/msdata/ChromatogramList_mz5.o \
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+./pwiz/data/msdata/examples.o \
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+./pwiz/data/msdata/Serializer_mzML.o \
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+./pwiz/data/msdata/Serializer_MSn.o \
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+./pwiz/data/msdata/Reader.o \
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+./pwiz/data/msdata/Serializer_mz5.o \
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+./pwiz/data/msdata/Serializer_MGF.o \
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+./pwiz/data/msdata/Serializer_mzXML.o \
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+./pwiz/data/msdata/SpectrumListBase.o \
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+./pwiz/data/msdata/SpectrumList_MGF.o \
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+./pwiz/data/msdata/SpectrumList_mzML.o \
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+./pwiz/data/msdata/SpectrumList_MSn.o \
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+./pwiz/data/msdata/SpectrumList_mz5.o \
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+./pwiz/data/msdata/BinaryDataEncoder.o \
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+./pwiz/data/msdata/Diff.o \
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+./pwiz/data/msdata/MSData.o \
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+./pwiz/data/msdata/References.o \
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+./pwiz/data/msdata/SpectrumList_mzXML.o \
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+./pwiz/data/msdata/IO.o \
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+./pwiz/data/msdata/SpectrumList_BTDX.o \
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+./pwiz/data/msdata/SpectrumInfo.o \
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+./pwiz/data/msdata/LegacyAdapter.o \
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+./pwiz/data/msdata/SpectrumIterator.o \
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+./pwiz/data/msdata/MSDataFile.o \
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+./pwiz/data/msdata/MSNumpress.o \
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+./pwiz/data/msdata/SpectrumListCache.o \
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+./pwiz/data/msdata/Index_mzML.o \
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+./pwiz/data/msdata/SpectrumWorkerThreads.o \
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+./pwiz/data/identdata/IdentDataFile.o \
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+./pwiz/data/identdata/IdentData.o \
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+./pwiz/data/identdata/DefaultReaderList.o \
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+./pwiz/data/identdata/Reader.o \
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+./pwiz/data/identdata/Serializer_protXML.o \
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+./pwiz/data/identdata/Serializer_pepXML.o \
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+./pwiz/data/identdata/Serializer_mzid.o \
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+./pwiz/data/identdata/IO.o \
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+./pwiz/data/identdata/References.o \
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+./pwiz/data/identdata/MascotReader.o \
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+./pwiz/data/proteome/Modification.o \
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+./pwiz/data/proteome/Digestion.o \
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+./pwiz/data/proteome/Peptide.o \
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+./pwiz/data/proteome/AminoAcid.o \
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+./pwiz/utility/minimxml/XMLWriter.o \
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+./pwiz/utility/minimxml/SAXParser.o \
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+./pwiz/utility/chemistry/Chemistry.o \
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+./pwiz/utility/chemistry/ChemistryData.o \
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+./pwiz/utility/chemistry/MZTolerance.o \
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+./pwiz/utility/misc/IntegerSet.o \
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+./pwiz/utility/misc/Base64.o \
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+./pwiz/utility/misc/BinaryData.o \
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+./pwiz/utility/misc/IterationListener.o \
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+./pwiz/utility/misc/MSIHandler.o \
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+./pwiz/utility/misc/Filesystem.o \
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+./pwiz/utility/misc/TabReader.o \
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+./pwiz/utility/misc/random_access_compressed_ifstream.o \
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+./pwiz/utility/misc/SHA1.o \
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+./pwiz/utility/misc/SHA1Calculator.o \
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+./pwiz/utility/misc/sha1calc.o \
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+./pwiz/utility/misc/String.o \
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+./RcppExports.o
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+
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+
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+ifeq ($(OS),Windows_NT)
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+ARCH_OBJS=./boost/libs/filesystem/src/path_traits.o \
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+./boost/libs/filesystem/src/windows_file_codecvt.o \
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+./boost/libs/filesystem/src/codecvt_error_category.o \
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+./boost/libs/thread/src/win32/tss_pe.o \
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+./boost/libs/thread/src/win32/tss_dll.o \
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+./boost/libs/thread/src/win32/thread.o \
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+./boost_aux/libs/nowide/src/iostream.o \
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+./boost_aux/libs/nowide/src/cstdio.o \
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+./boost_aux/libs/nowide/src/filebuf.o
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+ARCH_CPPFLAGS=-fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB
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+ARCH_LIBS=-lws2_32 -lz
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+RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)
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+else
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+ARCH_OBJS=./boost/libs/thread/src/pthread/once.o \
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+./boost/libs/thread/src/pthread/thread.o
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+RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)
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+endif
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+
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+MZROBJECTS= RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o
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+
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+OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) $(ARCH_OBJS)
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+
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+## Generate dependency files
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+#DEPFLAGS = -MT $@ -MMD -MP
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+
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+##
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+## R complains about assert(), hence -D_NODEBUG
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+##  http://www.gamedev.net/topic/555511-is-there-a-way-to-only-disable-boost-debug-checks/
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+##
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+
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+PWIZ_CPPFLAGS=-I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG
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+PWIZ_LDFLAGS=-lpthread
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+
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+## Use the R_HOME indirection to support installations of multiple R version
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+PKG_CPPFLAGS=$(PWIZ_CPPFLAGS) $(NC_CFLAGS)  $(ARCH_CPPFLAGS)
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+
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+PKG_LIBS=$(PWIZ_LDFLAGS) $(RHDF5_LIBS) $(NC_LIBS)  $(ARCH_LIBS)
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+
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+all: clean $(SHLIB)
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+
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+clean:
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+	rm -f $(OBJECTS)
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+
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new file mode 100755
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@@ -0,0 +1,74 @@
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+//
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+//  Copyright (c) 2012 Artyom Beilis (Tonkikh)
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+//  Copyright (c) 2020 Alexander Grund
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+//
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+//  Distributed under the Boost Software License, Version 1.0. (See
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+//  accompanying file LICENSE or copy at
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+//  http://www.boost.org/LICENSE_1_0.txt)
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+//
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+
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+#define BOOST_NOWIDE_SOURCE
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+
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+#ifdef _MSC_VER
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+#define _CRT_SECURE_NO_WARNINGS
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+#elif(defined(__MINGW32__) || defined(__CYGWIN__)) && defined(__STRICT_ANSI__)
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+// Need the _w* functions which are extensions on MinGW/Cygwin
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+#undef __STRICT_ANSI__
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+#endif
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+
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+#include <boost/nowide/cstdio.hpp>
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+#include <boost/nowide/stackstring.hpp>
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+
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+namespace boost {
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+namespace nowide {
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+    namespace detail {
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+        FILE* wfopen(const wchar_t* filename, const wchar_t* mode)
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+        {
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+#ifdef BOOST_WINDOWS
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+            return ::_wfopen(filename, mode);
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+#else
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+            const stackstring name(filename);
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+            const short_stackstring smode2(mode);
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+            return std::fopen(name.get(), smode2.get());
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+#endif
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+        }
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+    } // namespace detail
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+
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+#ifdef BOOST_WINDOWS
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+    ///
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+    /// \brief Same as freopen but file_name and mode are UTF-8 strings
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+    ///
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+    FILE* freopen(const char* file_name, const char* mode, FILE* stream)
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+    {
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+        const wstackstring wname(file_name);
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+        const wshort_stackstring wmode(mode);
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+        return _wfreopen(wname.get(), wmode.get(), stream);
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+    }
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+    ///
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+    /// \brief Same as fopen but file_name and mode are UTF-8 strings
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+    ///
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+    FILE* fopen(const char* file_name, const char* mode)
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+    {
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+        const wstackstring wname(file_name);
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+        const wshort_stackstring wmode(mode);
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+        return _wfopen(wname.get(), wmode.get());
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+    }
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+    ///
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+    /// \brief Same as rename but old_name and new_name are UTF-8 strings
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+    ///
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+    int rename(const char* old_name, const char* new_name)
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+    {
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+        const wstackstring wold(old_name), wnew(new_name);
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+        return _wrename(wold.get(), wnew.get());
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+    }
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+    ///
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+    /// \brief Same as rename but name is UTF-8 string
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+    ///
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+    int remove(const char* name)
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+    {
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+        const wstackstring wname(name);
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+        return _wremove(wname.get());
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+    }
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+#endif
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+} // namespace nowide
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+} // namespace boost
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new file mode 100755
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@@ -0,0 +1,80 @@
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+//
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+//  Copyright (c) 2020 Alexander Grund
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+//
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+//  Distributed under the Boost Software License, Version 1.0. (See
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+//  accompanying file LICENSE or copy at
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+//  http://www.boost.org/LICENSE_1_0.txt)
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+//
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+
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+#define BOOST_NOWIDE_SOURCE
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+
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+#ifdef BOOST_NOWIDE_NO_LFS
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+#define BOOST_NOWIDE_FTELL ::ftell
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+#define BOOST_NOWIDE_FSEEK ::fseek
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+#define BOOST_NOWIDE_OFF_T long
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+#elif defined(_WIN32) && !defined(__CYGWIN__) && !defined(__MINGW32__)
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+#define BOOST_NOWIDE_FTELL _ftelli64
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+#define BOOST_NOWIDE_FSEEK _fseeki64
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+#define BOOST_NOWIDE_OFF_T int64_t
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+#else
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+// IMPORTANT: Have these defines BEFORE any #includes
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+//            and make sure changes by those macros don't leak into the public interface
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+// Make LFS functions available
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+#define _LARGEFILE_SOURCE
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+// Make off_t 64 bits if the macro isn't set
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+#ifndef _FILE_OFFSET_BITS
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+#define _FILE_OFFSET_BITS 64
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+#endif
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+
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+#define BOOST_NOWIDE_FTELL ftello
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+#define BOOST_NOWIDE_FSEEK fseeko
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+#define BOOST_NOWIDE_OFF_T off_t
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+#endif
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+
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+#include <boost/nowide/filebuf.hpp>
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+#include <cassert>
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+#include <cstdint>
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+#include <limits>
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+#include <stdio.h>
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+#include <type_traits>
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+
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+namespace boost {
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+namespace nowide {
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+    namespace detail {
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+
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+        template<typename T, typename U>
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+        constexpr bool is_in_range(U value)
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+        {
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+            static_assert(std::is_signed<T>::value == std::is_signed<U>::value,
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+                          "Mixed sign comparison can lead to problems below");
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+            // coverity[result_independent_of_operands]
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+            return value >= std::numeric_limits<T>::min() && value <= std::numeric_limits<T>::max();
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+        }
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+
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+        template<typename T, typename U>
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+        T cast_if_valid_or_minus_one(U value)
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+        {
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+            return is_in_range<T>(value) ? static_cast<T>(value) : T(-1);
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+        }
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+
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+        std::streampos ftell(FILE* file)
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+        {
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+            const auto pos = BOOST_NOWIDE_FTELL(file);
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+            // Note that this is used in seekoff for which the standard states:
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+            // On success, it returns the new absolute position the internal position pointer points to after the call,
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+            // if representable [...] [or] the function returns pos_type(off_type(-1)). Hence we do a range check first,
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+            // then cast or return failure instead of silently truncating
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+            return cast_if_valid_or_minus_one<std::streamoff>(pos);
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+        }
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+
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+        int fseek(FILE* file, std::streamoff offset, int origin)
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+        {
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+            // Similar to above: If the value of offset can't fit inside target type
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+            // don't silently truncate but fail right away
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+            if(!is_in_range<BOOST_NOWIDE_OFF_T>(offset))
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+                return -1;
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+            return BOOST_NOWIDE_FSEEK(file, static_cast<BOOST_NOWIDE_OFF_T>(offset), origin);
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+        }
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+    } // namespace detail
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+} // namespace nowide
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+} // namespace boost