BioC 3.1: CHECK report for mzR on morelia

Package: mzR

Version: 2.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mzR_2.2.2.tar.gz

StartedAt: 2015-10-09 04:21:56 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:29:42 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 465.6 seconds

RetCode: 0

Status:  OK

CheckDir: mzR.Rcheck

Warnings: 0

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###
### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mzR_2.2.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/mzR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.2.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/win/i386/libnetcdf.a src/win/i386/libpwiz.a
  src/win/x64/libnetcdf.a src/win/x64/libpwiz.a
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... [397s/399s] OK
* checking installed package size ... NOTE
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
peaks,mzRpwiz : .local: no visible global function definition for
  ‘mising’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [5s/6s]
 [6s/6s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/mzR.Rcheck/00check.log’
for details.

* installing *source* package ‘mzR’ ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/src/pthread/once.o ./boost/thread/src/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./pwiz/data/msdata/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/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.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_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.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/RAMPAdapter.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/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/Version.o ./pwiz/data/identdata/References.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/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 ./random_access_gzFile.o rampR.o R_init_mzR.o
find . -name \*˜ -exec rm {} \;   ## from cleanup
find . -name \*.o -exec rm {} \;  ## from cleanup
find . -name "#*#" -exec rm {} \; ## from cleanup
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c cramp.cpp -o cramp.o
In file included from cramp.cpp:49:
./cramp.h:261:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ˜˜˜˜˜˜˜ ^
./cramp.h:261:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
./cramp.h:315:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ˜˜˜˜˜˜˜ ^
./cramp.h:315:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
cramp.cpp:73:27: warning: field 'm_declaredScansOnly' will be initialized after field 'm_runInfo' [-Wreorder]
    m_filename(fileName), m_declaredScansOnly(declaredScansOnly), m_runInfo()
                          ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ramp_base64.cpp -o ramp_base64.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c ramp.cpp -o ramp.o
ramp.cpp:248:23: warning: unused variable 'fgot' [-Wunused-variable]
                char *fgot=ramp_fgets(buf,sizeof(buf)-1,result);
                      ^
ramp.cpp:451:12: warning: unused variable 'nread' [-Wunused-variable]
    size_t nread = ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
           ^
ramp.cpp:650:31: warning: unused variable 'fgot' [-Wunused-variable]
                        char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                              ^
ramp.cpp:692:31: warning: unused variable 'fgot' [-Wunused-variable]
                        char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                              ^
ramp.cpp:729:27: warning: unused variable 'fgot' [-Wunused-variable]
                    char *fgot=ramp_fgets(buf, SIZE_BUF, pFI);
                          ^
ramp.cpp:1446:27: warning: unused variable 'fgot' [-Wunused-variable]
                    char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                          ^
ramp.cpp:1532:15: warning: unused variable 'fgot' [-Wunused-variable]
        char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
              ^
ramp.cpp:1528:11: warning: unused variable 'fgot' [-Wunused-variable]
    char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
          ^
ramp.cpp:2090:28: warning: unused variable 'nread' [-Wunused-variable]
                    size_t nread = ramp_fread(pData+partial,(int)(peaksLen-partial), pFI);
                           ^
ramp.cpp:2261:42: warning: expression which evaluates to zero treated as a null pointer constant of type 'const char *' [-Wnon-literal-null-conversion]
                        pEndAttrValue  = '\0';
                                         ^˜˜˜
ramp.cpp:2281:41: warning: expression which evaluates to zero treated as a null pointer constant of type 'const char *' [-Wnon-literal-null-conversion]
                        pEndAttrValue = '\0';
                                        ^˜˜˜
ramp.cpp:2293:27: warning: unused variable 'fgot' [-Wunused-variable]
                    char *fgot=ramp_fgets(buf, sizeof(buf)-1 , pFI);
                          ^
ramp.cpp:2340:24: warning: unused variable 'nread' [-Wunused-variable]
                size_t nread = ramp_fread(pData+partial,peaksLen-partial, pFI);
                       ^
ramp.cpp:2212:19: warning: unused variable 'fgot' [-Wunused-variable]
            char *fgot=ramp_fgets(buf, sizeof(buf)-1, pFI);
                  ^
ramp.cpp:2520:15: warning: unused variable 'fgot' [-Wunused-variable]
        char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
              ^
ramp.cpp:2544:15: warning: unused variable 'fgot' [-Wunused-variable]
        char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
              ^
ramp.cpp:2516:11: warning: unused variable 'fgot' [-Wunused-variable]
    char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
          ^
ramp.cpp:2695:19: warning: unused variable 'fgot' [-Wunused-variable]
            char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                  ^
ramp.cpp:2731:19: warning: unused variable 'fgot' [-Wunused-variable]
            char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
                  ^
ramp.cpp:2682:11: warning: unused variable 'fgot' [-Wunused-variable]
    char *fgot=ramp_fgets(stringBuf, SIZE_BUF, pFI);
          ^
20 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppRamp.cpp -o RcppRamp.o
In file included from RcppRamp.cpp:1:
In file included from ./RcppRamp.h:14:
./cramp.h:261:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ˜˜˜˜˜˜˜ ^
./cramp.h:261:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
./cramp.h:315:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ˜˜˜˜˜˜˜ ^
./cramp.h:315:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
RcppRamp.cpp:213:27: warning: unused variable 'info' [-Wunused-variable]
            rampScanInfo *info = ramp->getScanHeaderInfo( 1 );
                          ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppRampModule.cpp -o RcppRampModule.o
In file included from RcppRampModule.cpp:2:
In file included from ./RcppRamp.h:14:
./cramp.h:261:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampScanInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ˜˜˜˜˜˜˜ ^
./cramp.h:261:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
./cramp.h:315:17: warning: destination for this 'memmove' call is a pointer to dynamic class 'rampRunInfo'; vtable pointer will be overwritten [-Wdynamic-class-memaccess]
        memmove(this,&rhs,sizeof(rhs));
        ˜˜˜˜˜˜˜ ^
./cramp.h:315:17: note: explicitly cast the pointer to silence this warning
        memmove(this,&rhs,sizeof(rhs));
                ^
                (void*)
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rnetCDF.c -o rnetCDF.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppPwiz.cpp -o RcppPwiz.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppPwizModule.cpp -o RcppPwizModule.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppIdent.cpp -o RcppIdent.o
In file included from RcppIdent.cpp:1:
In file included from ./RcppIdent.h:11:
In file included from ./pwiz/data/identdata/IdentDataFile.hpp:29:
In file included from ./pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from RcppIdentModule.cpp:2:
In file included from ./RcppIdent.h:11:
In file included from ./pwiz/data/identdata/IdentDataFile.hpp:29:
In file included from ./pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/iostreams/src/file_descriptor.cpp -o boost/iostreams/src/file_descriptor.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/thread/src/pthread/once.cpp -o boost/thread/src/pthread/once.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/thread/src/pthread/thread.cpp -o boost/thread/src/pthread/thread.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
boost/filesystem/src/operations.cpp:250:21: warning: unused variable 'buf_size' [-Wunused-const-variable]
  const std::size_t buf_size(128);
                    ^
boost/filesystem/src/operations.cpp:323:8: warning: unused function 'error' [-Wunused-function]
  bool error(bool was_error, const error_code& result,
       ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/filesystem/src/path.cpp -o boost/filesystem/src/path.o
In file included from boost/filesystem/src/path.cpp:39:
In file included from ./boost/filesystem/detail/utf8_codecvt_facet.hpp:18:
./boost/detail/utf8_codecvt_facet.hpp:171:17: warning: 'boost::filesystem::detail::utf8_codecvt_facet::do_length' hides overloaded virtual function [-Woverloaded-virtual]
    virtual int do_length(
                ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:952:17: note: hidden overloaded virtual function 'std::__1::codecvt<wchar_t, char, __mbstate_t>::do_length' declared here: type mismatch at 1st parameter ('state_type &' (aka '__mbstate_t &') vs 'const std::mbstate_t &' (aka 'const __mbstate_t &'))
    virtual int do_length(state_type&, const extern_type* __frm, const extern_type* __end, size_t __mx) const;
                ^
boost/filesystem/src/path.cpp:76:21: warning: unused variable 'default_codecvt_buf_size' [-Wunused-const-variable]
  const std::size_t default_codecvt_buf_size = BOOST_FILESYSTEM_CODECVT_BUF_SIZE;
                    ^
boost/filesystem/src/path.cpp:101:14: warning: unused variable 'colon' [-Wunused-const-variable]
  const char colon = ':';
             ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c boost/filesystem/src/utf8_codecvt_facet.cpp -o boost/filesystem/src/utf8_codecvt_facet.o
In file included from boost/filesystem/src/utf8_codecvt_facet.cpp:23:
In file included from ./boost/detail/utf8_codecvt_facet.ipp:13:
./boost/detail/utf8_codecvt_facet.hpp:171:17: warning: 'boost::filesystem::detail::utf8_codecvt_facet::do_length' hides overloaded virtual function [-Woverloaded-virtual]
    virtual int do_length(
                ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:952:17: note: hidden overloaded virtual function 'std::__1::codecvt<wchar_t, char, __mbstate_t>::do_length' declared here: type mismatch at 1st parameter ('state_type &' (aka '__mbstate_t &') vs 'const std::mbstate_t &' (aka 'const __mbstate_t &'))
    virtual int do_length(state_type&, const extern_type* __frm, const extern_type* __end, size_t __mx) const;
                ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from pwiz/data/common/MemoryIndex.cpp:25:
In file included from pwiz/data/common/MemoryIndex.hpp:26:
In file included from pwiz/data/common/Index.hpp:30:
In file included from ./boost/shared_ptr.hpp:17:
In file included from ./boost/smart_ptr/shared_ptr.hpp:30:
./boost/checked_delete.hpp:34:5: warning: delete called on 'pwiz::data::MemoryIndex::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete x;
    ^
./boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete<pwiz::data::MemoryIndex::Impl>' requested here
            boost::checked_delete( p );
                   ^
./boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<pwiz::data::MemoryIndex::Impl>' requested here
    boost::detail::shared_count( p ).swap( pn );
    ^
./boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<pwiz::data::MemoryIndex::Impl, pwiz::data::MemoryIndex::Impl>' requested here
        boost::detail::sp_pointer_construct( this, p, pn );
                       ^
pwiz/data/common/MemoryIndex.cpp:73:44: note: in instantiation of function template specialization 'boost::shared_ptr<pwiz::data::MemoryIndex::Impl>::shared_ptr<pwiz::data::MemoryIndex::Impl>' requested here
PWIZ_API_DECL MemoryIndex::MemoryIndex() : impl_(new Impl) {}
                                           ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp:133:53: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/data/common/CVTranslator.cpp:133:53: note: place parentheses around the '&&' expression to silence this warning
    return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
                                                    ^
            (                                                       )
pwiz/data/common/CVTranslator.cpp:134:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
            key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/common/CVTranslator.cpp:134:40: note: place parentheses around the '&&' expression to silence this warning
            key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14
                                       ^
            (                                        )
pwiz/data/common/CVTranslator.cpp:135:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
            key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/common/CVTranslator.cpp:135:40: note: place parentheses around the '&&' expression to silence this warning
            key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
                                       ^
            (                                        )
pwiz/data/common/CVTranslator.cpp:136:40: warning: '&&' within '||' [-Wlogical-op-parentheses]
            key=="de_" && value==MS_DE && cvid==1001274); // conflict between 1000246 and 1001274
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/common/CVTranslator.cpp:136:40: note: place parentheses around the '&&' expression to silence this warning
            key=="de_" && value==MS_DE && cvid==1001274); // conflict between 1000246 and 1001274
                                       ^
            (                                          )
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from pwiz/data/common/BinaryIndexStream.cpp:25:
In file included from pwiz/data/common/BinaryIndexStream.hpp:26:
In file included from pwiz/data/common/Index.hpp:30:
In file included from ./boost/shared_ptr.hpp:17:
In file included from ./boost/smart_ptr/shared_ptr.hpp:30:
./boost/checked_delete.hpp:34:5: warning: delete called on 'pwiz::data::BinaryIndexStream::Impl' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete x;
    ^
./boost/smart_ptr/detail/shared_count.hpp:134:20: note: in instantiation of function template specialization 'boost::checked_delete<pwiz::data::BinaryIndexStream::Impl>' requested here
            boost::checked_delete( p );
                   ^
./boost/smart_ptr/shared_ptr.hpp:276:5: note: in instantiation of function template specialization 'boost::detail::shared_count::shared_count<pwiz::data::BinaryIndexStream::Impl>' requested here
    boost::detail::shared_count( p ).swap( pn );
    ^
./boost/smart_ptr/shared_ptr.hpp:354:24: note: in instantiation of function template specialization 'boost::detail::sp_pointer_construct<pwiz::data::BinaryIndexStream::Impl, pwiz::data::BinaryIndexStream::Impl>' requested here
        boost::detail::sp_pointer_construct( this, p, pn );
                       ^
pwiz/data/common/BinaryIndexStream.cpp:402:82: note: in instantiation of function template specialization 'boost::shared_ptr<pwiz::data::BinaryIndexStream::Impl>::shared_ptr<pwiz::data::BinaryIndexStream::Impl>' requested here
PWIZ_API_DECL BinaryIndexStream::BinaryIndexStream(shared_ptr<iostream> isPtr) : impl_(new Impl(isPtr)) {}
                                                                                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
pwiz/data/msdata/Serializer_MSn.cpp:43:11: warning: unused variable 'sizeChargeMSn' [-Wunused-const-variable]
const int sizeChargeMSn    = 12; // struct Charge{ int z; double mass; }
          ^
pwiz/data/msdata/Serializer_MSn.cpp:44:11: warning: unused variable 'sizePeakMSn' [-Wunused-const-variable]
const int sizePeakMSn      = 12; // struct Peak{ double mz; float intensity; }
          ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
pwiz/data/msdata/SpectrumList_mzML.cpp:59:25: warning: 'pwiz::msdata::<anonymous namespace>::SpectrumList_mzMLImpl::spectrum' hides overloaded virtual function [-Woverloaded-virtual]
    virtual SpectrumPtr spectrum(size_t index, IO::BinaryDataFlag binaryDataFlag, const SpectrumPtr *defaults) const;
                        ^
./pwiz/data/msdata/MSData.hpp:689:25: note: hidden overloaded virtual function 'pwiz::msdata::SpectrumList::spectrum' declared here: different number of parameters (2 vs 3)
    virtual SpectrumPtr spectrum(size_t index, DetailLevel detailLevel) const
                        ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
pwiz/data/msdata/IO.cpp:2013:35: warning: '&&' within '||' [-Wlogical-op-parentheses]
            else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
                     ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                ˜˜
pwiz/data/msdata/IO.cpp:2013:35: note: place parentheses around the '&&' expression to silence this warning
            else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
                                  ^
                     (                                        )
pwiz/data/msdata/IO.cpp:2722:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
        else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
                 ˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜                ˜˜
pwiz/data/msdata/IO.cpp:2722:31: note: place parentheses around the '&&' expression to silence this warning
        else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
                              ^
                 (                                            )
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
pwiz/data/msdata/SpectrumList_BTDX.cpp:276:19: warning: private field 'msd_' is not used [-Wunused-private-field]
    const MSData& msd_;
                  ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
pwiz/data/msdata/SpectrumIterator.cpp:125:20: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return (done() && &that.spectrumList_==&pastEndMarker_ ||
            ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/data/msdata/SpectrumIterator.cpp:125:20: note: place parentheses around the '&&' expression to silence this warning
    return (done() && &that.spectrumList_==&pastEndMarker_ ||
                   ^
            (                                             )
pwiz/data/msdata/SpectrumIterator.cpp:126:45: warning: '&&' within '||' [-Wlogical-op-parentheses]
            &spectrumList_==&pastEndMarker_ && that.done() ||
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/msdata/SpectrumIterator.cpp:126:45: note: place parentheses around the '&&' expression to silence this warning
            &spectrumList_==&pastEndMarker_ && that.done() ||
                                            ^
            (                                             )
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: '&&' within '||' [-Wlogical-op-parentheses]
            &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/data/msdata/SpectrumIterator.cpp:127:49: note: place parentheses around the '&&' expression to silence this warning
            &spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
                                                ^
            (                                                                       )
pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
           ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/data/msdata/SpectrumIterator.cpp:141:34: note: place parentheses around the '&&' expression to silence this warning
    return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
                                 ^
           (                                                              )
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
In file included from pwiz/data/msdata/SpectrumListCache.cpp:25:
pwiz/data/msdata/SpectrumListCache.hpp:43:52: warning: offset of on non-POD type 'KeyValuePair' (aka 'pair<size_t, SpectrumPtr>') [-Winvalid-offsetof]
    BOOST_STATIC_CONSTANT(unsigned, first_offset = offsetof(KeyValuePair, first));
                                                   ^                      ˜˜˜˜˜
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stddef.h:87:24: note: expanded from macro 'offsetof'
#define offsetof(t, d) __builtin_offsetof(t, d)
                       ^
./boost/config/suffix.hpp:394:72: note: expanded from macro 'BOOST_STATIC_CONSTANT'
#     define BOOST_STATIC_CONSTANT(type, assignment) static const type assignment
                                                                       ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from pwiz/data/identdata/IdentDataFile.cpp:25:
In file included from pwiz/data/identdata/IdentDataFile.hpp:29:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from pwiz/data/identdata/IdentData.cpp:31:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from pwiz/data/identdata/DefaultReaderList.cpp:29:
In file included from pwiz/data/identdata/DefaultReaderList.hpp:29:
In file included from pwiz/data/identdata/Reader.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from pwiz/data/identdata/Reader.cpp:26:
In file included from pwiz/data/identdata/Reader.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from pwiz/data/identdata/Serializer_protXML.cpp:28:
In file included from pwiz/data/identdata/Serializer_protXML.hpp:29:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
pwiz/data/identdata/Serializer_protXML.cpp:97:9: warning: field 'strict' will be initialized after field 'nPeptides' [-Wreorder]
        strict(strict),
        ^
pwiz/data/identdata/Serializer_protXML.cpp:476:10: warning: private field 'readSpectrumQueries' is not used [-Wunused-private-field]
    bool readSpectrumQueries;
         ^
pwiz/data/identdata/Serializer_protXML.cpp:477:38: warning: private field 'ilr' is not used [-Wunused-private-field]
    const IterationListenerRegistry* ilr;
                                     ^
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from pwiz/data/identdata/Serializer_pepXML.cpp:25:
In file included from pwiz/data/identdata/Serializer_pepXML.hpp:27:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
pwiz/data/identdata/Serializer_pepXML.cpp:553:104: warning: adding 'char' to a string does not append to the string [-Wstring-plus-int]
                        default: throw runtime_error("[write_search_summary] Unsupported AA residue: " + aa);
                                                     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜
pwiz/data/identdata/Serializer_pepXML.cpp:553:104: note: use array indexing to silence this warning
                        default: throw runtime_error("[write_search_summary] Unsupported AA residue: " + aa);
                                                                                                       ^
                                                     &                                                 [   ]
pwiz/data/identdata/Serializer_pepXML.cpp:975:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
    const CVTranslator& _cvTranslator;
                        ^
pwiz/data/identdata/Serializer_pepXML.cpp:1373:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
    const CVTranslator& _cvTranslator;
                        ^
pwiz/data/identdata/Serializer_pepXML.cpp:1717:25: warning: private field '_cvTranslator' is not used [-Wunused-private-field]
    const CVTranslator& _cvTranslator;
                        ^
pwiz/data/identdata/Serializer_pepXML.cpp:1887:38: warning: private field 'ilr' is not used [-Wunused-private-field]
    const IterationListenerRegistry* ilr;
                                     ^
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from pwiz/data/identdata/Serializer_mzid.cpp:26:
In file included from pwiz/data/identdata/Serializer_mzid.hpp:28:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from pwiz/data/identdata/IO.cpp:26:
In file included from pwiz/data/identdata/IO.hpp:27:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from pwiz/data/identdata/References.cpp:25:
In file included from pwiz/data/identdata/References.hpp:29:
In file included from pwiz/data/identdata/IdentData.hpp:30:
In file included from ./pwiz/data/proteome/Digestion.hpp:32:
In file included from ./pwiz/data/proteome/Peptide.hpp:183:
./pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
pwiz/data/identdata/References.cpp:149:13: warning: add explicit braces to avoid dangling else [-Wdangling-else]
            BOOST_FOREACH(OrganizationPtr& org, static_cast<Person*>(c.get())->affiliations)
            ^
./boost/foreach.hpp:1100:5: note: expanded from macro 'BOOST_FOREACH'
    BOOST_FOREACH_PREAMBLE()                                                                                      \
    ^
./boost/foreach.hpp:955:63: note: expanded from macro 'BOOST_FOREACH_PREAMBLE'
    if (bool BOOST_FOREACH_ID(_foreach_is_rvalue) = false) {} else
                                                              ^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from pwiz/data/proteome/Modification.cpp:27:
pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from pwiz/data/proteome/Digestion.cpp:27:
In file included from pwiz/data/proteome/Digestion.hpp:32:
In file included from pwiz/data/proteome/Peptide.hpp:183:
pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from pwiz/data/proteome/Peptide.cpp:26:
In file included from pwiz/data/proteome/Peptide.hpp:183:
pwiz/data/proteome/Modification.hpp:189:18: warning: 'pwiz::proteome::ModificationMap::swap' hides overloaded virtual function [-Woverloaded-virtual]
    virtual void swap(ModificationMap&);
                 ^
./pwiz/utility/misc/virtual_map.hpp:218:18: note: hidden overloaded virtual function 'pwiz::util::virtual_map<int, pwiz::proteome::ModificationList, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, pwiz::proteome::ModificationList> > >::swap' declared here: type mismatch at 1st parameter ('virtual_map<int, pwiz::proteome::ModificationList, key_compare, allocator_type> &' vs 'pwiz::proteome::ModificationMap &')
    virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
                 ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
pwiz/utility/misc/IntegerSet.cpp:307:63: warning: '&&' within '||' [-Wlogical-op-parentheses]
    return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
            ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜˜
pwiz/utility/misc/IntegerSet.cpp:307:63: note: place parentheses around the '&&' expression to silence this warning
    return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
                                                              ^
            (                                                                       )
pwiz/utility/misc/IntegerSet.cpp:308:23: warning: '&&' within '||' [-Wlogical-op-parentheses]
            it_==end_ && that.it_==nothing_.end());
            ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
pwiz/utility/misc/IntegerSet.cpp:308:23: note: place parentheses around the '&&' expression to silence this warning
            it_==end_ && that.it_==nothing_.end());
                      ^
            (                                    )
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
pwiz/utility/misc/TabReader.cpp:44:22: warning: assigning field to itself [-Wself-assign-field]
        comment_char = comment_char;
                     ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from pwiz/utility/misc/random_access_compressed_ifstream.cpp:85:
In file included from ./boost/filesystem/detail/utf8_codecvt_facet.hpp:18:
./boost/detail/utf8_codecvt_facet.hpp:171:17: warning: 'boost::filesystem::detail::utf8_codecvt_facet::do_length' hides overloaded virtual function [-Woverloaded-virtual]
    virtual int do_length(
                ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:952:17: note: hidden overloaded virtual function 'std::__1::codecvt<wchar_t, char, __mbstate_t>::do_length' declared here: type mismatch at 1st parameter ('state_type &' (aka '__mbstate_t &') vs 'const std::mbstate_t &' (aka 'const __mbstate_t &'))
    virtual int do_length(state_type&, const extern_type* __frm, const extern_type* __end, size_t __mx) const;
                ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from pwiz/utility/misc/sha1calc.cpp:25:
In file included from pwiz/utility/misc/unit.hpp:35:
In file included from ./boost/filesystem/detail/utf8_codecvt_facet.hpp:18:
./boost/detail/utf8_codecvt_facet.hpp:171:17: warning: 'boost::filesystem::detail::utf8_codecvt_facet::do_length' hides overloaded virtual function [-Woverloaded-virtual]
    virtual int do_length(
                ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:952:17: note: hidden overloaded virtual function 'std::__1::codecvt<wchar_t, char, __mbstate_t>::do_length' declared here: type mismatch at 1st parameter ('state_type &' (aka '__mbstate_t &') vs 'const std::mbstate_t &' (aka 'const __mbstate_t &'))
    virtual int do_length(state_type&, const extern_type* __frm, const extern_type* __end, size_t __mx) const;
                ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c random_access_gzFile.cpp -o random_access_gzFile.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c rampR.cpp -o rampR.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -DWITHOUT_MZ5 -I./boost `nc-config --cflags || /bin/true` -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_mzR.c -o R_init_mzR.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o mzR.so cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.o RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/system/src/error_code.o ./boost/regex/src/posix_api.o ./boost/regex/src/fileiter.o ./boost/regex/src/regex_raw_buffer.o ./boost/regex/src/cregex.o ./boost/regex/src/regex_debug.o ./boost/regex/src/instances.o ./boost/regex/src/icu.o ./boost/regex/src/usinstances.o ./boost/regex/src/regex.o ./boost/regex/src/wide_posix_api.o ./boost/regex/src/regex_traits_defaults.o ./boost/regex/src/winstances.o ./boost/regex/src/wc_regex_traits.o ./boost/regex/src/c_regex_traits.o ./boost/regex/src/cpp_regex_traits.o ./boost/regex/src/static_mutex.o ./boost/regex/src/w32_regex_traits.o ./boost/iostreams/src/zlib.o ./boost/iostreams/src/file_descriptor.o ./boost/thread/src/pthread/once.o ./boost/thread/src/pthread/thread.o ./boost/filesystem/src/operations.o ./boost/filesystem/src/path.o ./boost/filesystem/src/utf8_codecvt_facet.o ./pwiz/data/msdata/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/SpectrumList_MGF.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.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_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.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/RAMPAdapter.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/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/Version.o ./pwiz/data/identdata/References.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/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 ./random_access_gzFile.o rampR.o R_init_mzR.o -lpthread -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-3.1-bioc/meat/mzR.Rcheck/mzR/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘close’ from package ‘base’ in package ‘mzR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mzR)

name	user	system	elapsed
metadata	0.137	0.011	0.270
mzR-class	0.078	0.009	0.087
openMSfile	0.138	0.008	0.146
peaks	0.057	0.007	0.064