@@ -39,7 +39,6 @@ Suggests:

 VignetteBuilder: knitr

 LinkingTo:

     Rcpp,

-    zlibbioc,

     Rhdf5lib (>= 1.1.4)

 RcppModules:

     Pwiz,

@@ -38,6 +38,8 @@ PWIZOBJECTS=\

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

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

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

+./boost_aux/boost/nowide/filebuf.o \

+./boost_aux/libs/nowide/src/cstdio.o \

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

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

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

@@ -105,6 +107,6 @@ all: libpwiz.a

 libpwiz.a: $(PWIZOBJECTS)

 	ar -rc $@ $(PWIZOBJECTS)

-	

+

 clean:

-	rm -rf $(PWIZOBJECTS)

\ No newline at end of file

+	rm -rf $(PWIZOBJECTS)

@@ -102,14 +102,21 @@ ARCH_OBJS=./boost/libs/filesystem/src/path_traits.o \

 ./boost/libs/thread/src/win32/tss_pe.o \

 ./boost/libs/thread/src/win32/tss_dll.o \

 ./boost/libs/thread/src/win32/thread.o \

-./boost_aux/libs/nowide/src/iostream.o

+./boost_aux/libs/nowide/src/iostream.o \

+./boost_aux/libs/nowide/src/cstdio.o \

+./boost_aux/libs/nowide/src/filebuf.o

 ARCH_CPPFLAGS=-fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB

 ARCH_LIBS=-lws2_32 -lz

-RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)  

+RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)

+ZLIB_CFLAGS=$(shell echo 'zlibbioc::pkgconfig("PKG_CFLAGS")'| "${R_HOME}/bin/R" --vanilla --slave)

+ZLIB_LIBS=$(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_shared")' | "${R_HOME}/bin/R" --vanilla --slave)

 else

 ARCH_OBJS=./boost/libs/thread/src/pthread/once.o \

 ./boost/libs/thread/src/pthread/thread.o

 RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)

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

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

+ZLIB_LIBS=$(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_shared")' | "${R_HOME}/bin/R" --vanilla --slave)

 endif

 MZROBJECTS= RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o

@@ -117,7 +124,7 @@ MZROBJECTS= RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o

 OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) $(ARCH_OBJS)

 ## Generate dependency files

-#DEPFLAGS = -MT $@ -MMD -MP 

+#DEPFLAGS = -MT $@ -MMD -MP

 ##

 ## R complains about assert(), hence -D_NODEBUG

new file mode 100644

@@ -0,0 +1,141 @@

+PWIZOBJECTS=\

+./boost/libs/system/src/error_code.o \

+./boost/libs/regex/src/posix_api.o \

+./boost/libs/regex/src/regex_debug.o \

+./boost/libs/regex/src/regex.o \

+./boost/libs/regex/src/wide_posix_api.o \

+./boost/libs/regex/src/static_mutex.o \

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

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

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

+./boost/libs/filesystem/src/directory.o \

+./boost/libs/filesystem/src/exception.o \

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

+./boost/libs/filesystem/src/unique_path.o \

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

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

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

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

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

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

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

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

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

+./pwiz/data/common/ParamTypes.o \

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

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

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

+./pwiz/data/msdata/mz5/Configuration_mz5.o \

+./pwiz/data/msdata/mz5/Connection_mz5.o \

+./pwiz/data/msdata/mz5/Datastructures_mz5.o \

+./pwiz/data/msdata/mz5/ReferenceRead_mz5.o \

+./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o \

+./pwiz/data/msdata/mz5/Translator_mz5.o \

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

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

+./pwiz/data/msdata/ChromatogramList_mz5.o \

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

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

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

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

+./pwiz/data/msdata/Serializer_mz5.o \

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

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

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

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

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

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

+./pwiz/data/msdata/SpectrumList_mz5.o \

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

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

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

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

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

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

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

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

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

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

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

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

+./pwiz/data/identdata/Reader.o \

+./pwiz/data/identdata/Serializer_protXML.o \

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

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

+./pwiz/data/identdata/IO.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 \

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

+./pwiz/utility/misc/Base64.o \

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

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

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

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

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

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

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

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

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

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

+./RcppExports.o

+

+

+ifeq ($(OS),Windows_NT)

+ARCH_OBJS=./boost/libs/filesystem/src/path_traits.o \

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

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

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

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

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

+./boost_aux/libs/nowide/src/iostream.o \

+./boost_aux/libs/nowide/src/cstdio.o \

+./boost_aux/libs/nowide/src/filebuf.o

+ARCH_CPPFLAGS=-fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB

+ARCH_LIBS=-lws2_32 -lz

+RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)

+else

+ARCH_OBJS=./boost/libs/thread/src/pthread/once.o \

+./boost/libs/thread/src/pthread/thread.o

+RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave)

+endif

+

+MZROBJECTS= RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o

+

+OBJECTS= $(MZROBJECTS) $(PWIZOBJECTS) $(ARCH_OBJS)

+

+## Generate dependency files

+#DEPFLAGS = -MT $@ -MMD -MP

+

+##

+## R complains about assert(), hence -D_NODEBUG

+##  http://www.gamedev.net/topic/555511-is-there-a-way-to-only-disable-boost-debug-checks/

+##

+

+PWIZ_CPPFLAGS=-I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG

+PWIZ_LDFLAGS=-lpthread

+

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

+PKG_CPPFLAGS=$(PWIZ_CPPFLAGS) $(NC_CFLAGS)  $(ARCH_CPPFLAGS)

+

+PKG_LIBS=$(PWIZ_LDFLAGS) $(RHDF5_LIBS) $(NC_LIBS)  $(ARCH_LIBS)

+

+all: clean $(SHLIB)

+

+clean:

+	rm -f $(OBJECTS)

+

new file mode 100755

@@ -0,0 +1,74 @@

+//

+//  Copyright (c) 2012 Artyom Beilis (Tonkikh)

+//  Copyright (c) 2020 Alexander Grund

+//

+//  Distributed under the Boost Software License, Version 1.0. (See

+//  accompanying file LICENSE or copy at

+//  http://www.boost.org/LICENSE_1_0.txt)

+//

+

+#define BOOST_NOWIDE_SOURCE

+

+#ifdef _MSC_VER

+#define _CRT_SECURE_NO_WARNINGS

+#elif(defined(__MINGW32__) || defined(__CYGWIN__)) && defined(__STRICT_ANSI__)

+// Need the _w* functions which are extensions on MinGW/Cygwin

+#undef __STRICT_ANSI__

+#endif

+

+#include <boost/nowide/cstdio.hpp>

+#include <boost/nowide/stackstring.hpp>

+

+namespace boost {

+namespace nowide {

+    namespace detail {

+        FILE* wfopen(const wchar_t* filename, const wchar_t* mode)

+        {

+#ifdef BOOST_WINDOWS

+            return ::_wfopen(filename, mode);

+#else

+            const stackstring name(filename);

+            const short_stackstring smode2(mode);

+            return std::fopen(name.get(), smode2.get());

+#endif

+        }

+    } // namespace detail

+

+#ifdef BOOST_WINDOWS

+    ///

+    /// \brief Same as freopen but file_name and mode are UTF-8 strings

+    ///

+    FILE* freopen(const char* file_name, const char* mode, FILE* stream)

+    {

+        const wstackstring wname(file_name);

+        const wshort_stackstring wmode(mode);

+        return _wfreopen(wname.get(), wmode.get(), stream);

+    }

+    ///

+    /// \brief Same as fopen but file_name and mode are UTF-8 strings

+    ///

+    FILE* fopen(const char* file_name, const char* mode)

+    {

+        const wstackstring wname(file_name);

+        const wshort_stackstring wmode(mode);

+        return _wfopen(wname.get(), wmode.get());

+    }

+    ///

+    /// \brief Same as rename but old_name and new_name are UTF-8 strings

+    ///

+    int rename(const char* old_name, const char* new_name)

+    {

+        const wstackstring wold(old_name), wnew(new_name);

+        return _wrename(wold.get(), wnew.get());

+    }

+    ///

+    /// \brief Same as rename but name is UTF-8 string

+    ///

+    int remove(const char* name)

+    {

+        const wstackstring wname(name);

+        return _wremove(wname.get());

+    }

+#endif

+} // namespace nowide

+} // namespace boost

new file mode 100755

@@ -0,0 +1,80 @@

+//

+//  Copyright (c) 2020 Alexander Grund

+//

+//  Distributed under the Boost Software License, Version 1.0. (See

+//  accompanying file LICENSE or copy at

+//  http://www.boost.org/LICENSE_1_0.txt)

+//

+

+#define BOOST_NOWIDE_SOURCE

+

+#ifdef BOOST_NOWIDE_NO_LFS

+#define BOOST_NOWIDE_FTELL ::ftell

+#define BOOST_NOWIDE_FSEEK ::fseek

+#define BOOST_NOWIDE_OFF_T long

+#elif defined(_WIN32) && !defined(__CYGWIN__) && !defined(__MINGW32__)

+#define BOOST_NOWIDE_FTELL _ftelli64

+#define BOOST_NOWIDE_FSEEK _fseeki64

+#define BOOST_NOWIDE_OFF_T int64_t

+#else

+// IMPORTANT: Have these defines BEFORE any #includes

+//            and make sure changes by those macros don't leak into the public interface

+// Make LFS functions available

+#define _LARGEFILE_SOURCE

+// Make off_t 64 bits if the macro isn't set

+#ifndef _FILE_OFFSET_BITS

+#define _FILE_OFFSET_BITS 64

+#endif

+

+#define BOOST_NOWIDE_FTELL ftello

+#define BOOST_NOWIDE_FSEEK fseeko

+#define BOOST_NOWIDE_OFF_T off_t

+#endif

+

+#include <boost/nowide/filebuf.hpp>

+#include <cassert>

+#include <cstdint>

+#include <limits>

+#include <stdio.h>

+#include <type_traits>

+

+namespace boost {

+namespace nowide {

+    namespace detail {

+

+        template<typename T, typename U>

+        constexpr bool is_in_range(U value)

+        {

+            static_assert(std::is_signed<T>::value == std::is_signed<U>::value,

+                          "Mixed sign comparison can lead to problems below");

+            // coverity[result_independent_of_operands]

+            return value >= std::numeric_limits<T>::min() && value <= std::numeric_limits<T>::max();

+        }

+

+        template<typename T, typename U>

+        T cast_if_valid_or_minus_one(U value)

+        {

+            return is_in_range<T>(value) ? static_cast<T>(value) : T(-1);

+        }

+

+        std::streampos ftell(FILE* file)

+        {

+            const auto pos = BOOST_NOWIDE_FTELL(file);

+            // Note that this is used in seekoff for which the standard states:

+            // On success, it returns the new absolute position the internal position pointer points to after the call,

+            // if representable [...] [or] the function returns pos_type(off_type(-1)). Hence we do a range check first,

+            // then cast or return failure instead of silently truncating

+            return cast_if_valid_or_minus_one<std::streamoff>(pos);

+        }

+

+        int fseek(FILE* file, std::streamoff offset, int origin)

+        {

+            // Similar to above: If the value of offset can't fit inside target type

+            // don't silently truncate but fail right away

+            if(!is_in_range<BOOST_NOWIDE_OFF_T>(offset))

+                return -1;

+            return BOOST_NOWIDE_FSEEK(file, static_cast<BOOST_NOWIDE_OFF_T>(offset), origin);

+        }

+    } // namespace detail

+} // namespace nowide

+} // namespace boost