mzR 1.2.2
Bernd Fischer
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/mzR | | Last Changed Rev: 67123 / Revision: 69725 | | Last Changed Date: 2012-06-28 12:18:23 -0700 (Thu, 28 Jun 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.10-bioc/meat/mzR.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mzR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mzR' version '1.2.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'mzR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.0Mb
sub-directories of 1Mb or more:
libs 8.6Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for unstated 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
File 'mzR/R/zzz.R':
.onLoad calls:
require("methods", character = TRUE, quietly = TRUE)
Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.
.onLoad: warning in require("methods", character = TRUE, quietly =
TRUE): partial argument match of 'character' to 'character.only'
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-2.10-bioc/meat/mzR.buildbin-libdir/mzR/libs/i386/mzR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'E:/biocbld/bbs-2.10-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64/mzR.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
'Makefile'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
Running 'doRUnit.R'
OK
** running tests for arch 'x64'
Running 'doRUnit.R'
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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
'E:/biocbld/bbs-2.10-bioc/meat/mzR.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'mzR' ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.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 ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/filesystem/src/operations.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/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/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.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
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c cramp.cpp -o cramp.o
cramp.cpp:4:1: warning: "/*" within comment [-Wcomment]
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:143:9: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
cramp.h:142:17: warning: 'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
cramp.cpp:59:1: warning: when initialized here [-Wreorder]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c ramp_base64.cpp -o ramp_base64.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c ramp.cpp -o ramp.o
ramp.cpp:67:0: warning: "S_ISDIR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/sys/stat.h:155:0: note: this is the location of the previous definition
ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
ramp.cpp:201:18: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
ramp.cpp:378:11: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
ramp.cpp:555:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:591:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:627:19: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
ramp.cpp:1206:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1284:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:1280:10: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1778:23: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp:1919:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
ramp.cpp:1938:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
ramp.cpp:1951:21: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:1995:17: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp:2043:15: warning: variable 'err' set but not used [-Wunused-but-set-variable]
ramp.cpp:1876:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
ramp.cpp:2153:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2173:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2149:10: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
ramp.cpp:2315:16: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2351:15: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2305:10: warning: unused variable 'fgot' [-Wunused-variable]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c RcppRamp.cpp -o RcppRamp.o
RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()':
RcppRamp.cpp:170:21: warning: unused variable 'info' [-Wunused-variable]
RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)':
RcppRamp.cpp:309:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -D_LARGEFILE_SOURCE -I./win//i386 -D_MSC_VER -DWIN32_LEAN_AND_MEAN -fgnu89-inline -O3 -Wall -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
pwiz/utility/minimxml/XMLWriter.cpp: In member function 'void pwiz::minimxml::XMLWriter::Impl::startElement(const string&, const Attributes&, pwiz::minimxml::XMLWriter::EmptyElementTag)':
pwiz/utility/minimxml/XMLWriter.cpp:160:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:134:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:135:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:136:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/thread/win32/once.hpp:18:0,
from ./boost/thread/once.hpp:14,
from ./boost_aux/boost/utility/detail/singleton_manager.hpp:18,
from ./boost_aux/boost/utility/singleton.hpp:19,
from pwiz/data/common/cv.cpp:32:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
In file included from ./boost/thread/once.hpp:14:0,
from ./boost_aux/boost/utility/detail/singleton_manager.hpp:18,
from ./boost_aux/boost/utility/singleton.hpp:19,
from pwiz/data/common/cv.cpp:32:
./boost/thread/win32/once.hpp: In function 'void boost::call_once(boost::once_flag&, Function) [with Function = void (*)()]':
./boost/thread/once.hpp:27:28: instantiated from here
./boost/thread/win32/once.hpp:172:21: warning: value computed is not used [-Wunused-value]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/thread/win32/thread_data.hpp:11:0,
from ./boost/thread/thread.hpp:15,
from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
In file included from ./boost/thread/shared_mutex.hpp:14:0,
from ./boost/thread/detail/thread_group.hpp:9,
from ./boost/thread/thread.hpp:24,
from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/thread/win32/shared_mutex.hpp:102:103: instantiated from here
./boost/thread/win32/shared_mutex.hpp:48:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:48:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:49:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:49:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./boost/thread/win32/once.hpp:18:0,
from ./boost/thread/once.hpp:14,
from ./pwiz/utility/misc/Once.hpp:25,
from pwiz/data/msdata/SpectrumList_mzML.cpp:31:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
In file included from ./boost/thread/once.hpp:14:0,
from ./pwiz/utility/misc/Once.hpp:25,
from pwiz/data/msdata/SpectrumList_mzML.cpp:31:
./boost/thread/win32/once.hpp: In function 'void boost::call_once(boost::once_flag&, Function) [with Function = void (*)()]':
./boost/thread/once.hpp:27:28: instantiated from here
./boost/thread/win32/once.hpp:172:21: warning: value computed is not used [-Wunused-value]
./boost/thread/win32/once.hpp: In function 'void boost::call_once(boost::once_flag&, Function) [with Function = boost::_bi::bind_t<void, boost::_mfi::cmf0<void, pwiz::msdata::{anonymous}::SpectrumList_mzMLImpl>, boost::_bi::list1<boost::_bi::value<const pwiz::msdata::{anonymous}::SpectrumList_mzMLImpl*> > >]':
pwiz/data/msdata/SpectrumList_mzML.cpp:94:97: instantiated from here
./boost/thread/win32/once.hpp:172:21: warning: value computed is not used [-Wunused-value]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:1939:86: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2644:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
pwiz/data/msdata/ramp/wglob.cpp: In function 'int glob(const char*, int, int*, glob_t*)':
pwiz/data/msdata/ramp/wglob.cpp:63:9: warning: unused variable 'fileList' [-Wunused-variable]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const':
pwiz/data/msdata/SpectrumIterator.cpp:126:58: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp:127:72: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:142:48: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const':
pwiz/utility/misc/IntegerSet.cpp:308:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
pwiz/utility/misc/IterationListener.cpp: In member function 'pwiz::util::IterationListener::Status pwiz::util::IterationListenerRegistry::Impl::broadcastUpdateMessage(const pwiz::util::IterationListener::UpdateMessage&) const':
pwiz/utility/misc/IterationListener.cpp:76:94: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/utility/misc/IterationListener.cpp:78:87: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
pwiz/utility/misc/Filesystem.cpp:36:0: warning: "_WIN32_WINNT" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/_mingw.h:244:0: note: this is the location of the previous definition
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -O2 -Wall -mtune=core2 -c rampR.cpp -o rampR.o
g++ -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.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 ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/filesystem/src/operations.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/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/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.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 E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/lib/i386/libRcpp.a -L./win//i386 -lws2_32 -lnetcdf -lz -LE:/biocbld/BBS-2˜1.10-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/mzR.buildbin-libdir/mzR/libs/i386
** 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
'mzR.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'mzR' ...
** libs
rm -f cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.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 ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/filesystem/src/operations.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/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/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.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
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c cramp.cpp -o cramp.o
cramp.cpp:4:1: warning: "/*" within comment [-Wcomment]
cramp.h: In constructor 'cRamp::cRamp(const char*, bool)':
cramp.h:143:9: warning: 'cRamp::m_declaredScansOnly' will be initialized after [-Wreorder]
cramp.h:142:17: warning: 'rampRunInfo* cRamp::m_runInfo' [-Wreorder]
cramp.cpp:59:1: warning: when initialized here [-Wreorder]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ramp_base64.cpp -o ramp_base64.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c ramp.cpp -o ramp.o
ramp.cpp:67:0: warning: "S_ISDIR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/sys/stat.h:155:0: note: this is the location of the previous definition
ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
ramp.cpp:201:18: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
ramp.cpp:378:11: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
ramp.cpp:555:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:591:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:627:19: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
ramp.cpp:1206:22: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1284:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:1280:10: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
ramp.cpp:1778:23: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp:1919:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
ramp.cpp:1938:31: warning: variable 'pEndAttrValue' set but not used [-Wunused-but-set-variable]
ramp.cpp:1951:21: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:1995:17: warning: unused variable 'nread' [-Wunused-variable]
ramp.cpp:2043:15: warning: variable 'err' set but not used [-Wunused-but-set-variable]
ramp.cpp:1876:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
ramp.cpp:2153:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2173:13: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2149:10: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
ramp.cpp:2315:16: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2351:15: warning: unused variable 'fgot' [-Wunused-variable]
ramp.cpp:2305:10: warning: unused variable 'fgot' [-Wunused-variable]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c RcppRamp.cpp -o RcppRamp.o
RcppRamp.cpp: In member function 'Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo()':
RcppRamp.cpp:170:21: warning: unused variable 'info' [-Wunused-variable]
RcppRamp.cpp: In member function 'Rcpp::NumericMatrix RcppRamp::get3DMap(std::vector<int>, double, double, double)':
RcppRamp.cpp:309:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c RcppRampModule.cpp -o RcppRampModule.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -D_LARGEFILE_SOURCE -I./win//x64 -D_MSC_VER -DWIN32_LEAN_AND_MEAN -fgnu89-inline -O2 -Wall -std=gnu99 -mtune=core2 -c rnetCDF.c -o rnetCDF.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/system/src/error_code.cpp -o boost/system/src/error_code.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/fileiter.cpp -o boost/regex/src/fileiter.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_raw_buffer.cpp -o boost/regex/src/regex_raw_buffer.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/cregex.cpp -o boost/regex/src/cregex.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_debug.cpp -o boost/regex/src/regex_debug.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/instances.cpp -o boost/regex/src/instances.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/icu.cpp -o boost/regex/src/icu.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/usinstances.cpp -o boost/regex/src/usinstances.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex.cpp -o boost/regex/src/regex.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/wide_posix_api.cpp -o boost/regex/src/wide_posix_api.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/regex_traits_defaults.cpp -o boost/regex/src/regex_traits_defaults.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/winstances.cpp -o boost/regex/src/winstances.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/wc_regex_traits.cpp -o boost/regex/src/wc_regex_traits.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/c_regex_traits.cpp -o boost/regex/src/c_regex_traits.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/cpp_regex_traits.cpp -o boost/regex/src/cpp_regex_traits.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/static_mutex.cpp -o boost/regex/src/static_mutex.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/regex/src/w32_regex_traits.cpp -o boost/regex/src/w32_regex_traits.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
pwiz/utility/minimxml/XMLWriter.cpp: In member function 'void pwiz::minimxml::XMLWriter::Impl::startElement(const string&, const Attributes&, pwiz::minimxml::XMLWriter::EmptyElementTag)':
pwiz/utility/minimxml/XMLWriter.cpp:160:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/iostreams/src/zlib.cpp -o boost/iostreams/src/zlib.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c boost/filesystem/src/operations.cpp -o boost/filesystem/src/operations.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:134:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:135:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/common/CVTranslator.cpp:136:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/thread/win32/once.hpp:18:0,
from ./boost/thread/once.hpp:14,
from ./boost_aux/boost/utility/detail/singleton_manager.hpp:18,
from ./boost_aux/boost/utility/singleton.hpp:19,
from pwiz/data/common/cv.cpp:32:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/thread/win32/thread_data.hpp:11:0,
from ./boost/thread/thread.hpp:15,
from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
In file included from ./boost/thread/shared_mutex.hpp:14:0,
from ./boost/thread/detail/thread_group.hpp:9,
from ./boost/thread/thread.hpp:24,
from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/win32/shared_mutex.hpp: In member function 'T boost::shared_mutex::interlocked_compare_exchange(T*, T, T) [with T = boost::shared_mutex::state_data]':
./boost/thread/win32/shared_mutex.hpp:102:103: instantiated from here
./boost/thread/win32/shared_mutex.hpp:48:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:48:99: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:49:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
./boost/thread/win32/shared_mutex.hpp:49:52: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./boost/thread/win32/once.hpp:18:0,
from ./boost/thread/once.hpp:14,
from ./pwiz/utility/misc/Once.hpp:25,
from pwiz/data/msdata/SpectrumList_mzML.cpp:31:
./boost/thread/win32/thread_primitives.hpp:123:73: warning: declaration of 'void boost::detail::win32::Sleep(long unsigned int)' with C language linkage [enabled by default]
./boost/smart_ptr/detail/yield_k.hpp:58:29: warning: conflicts with previous declaration 'void boost::detail::Sleep(unsigned int)' [enabled by default]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:1939:86: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2644:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/RAMPAdapter.cpp -o pwiz/data/msdata/RAMPAdapter.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/ramp/wglob.cpp -o pwiz/data/msdata/ramp/wglob.o
pwiz/data/msdata/ramp/wglob.cpp: In function 'int glob(const char*, int, int*, glob_t*)':
pwiz/data/msdata/ramp/wglob.cpp:63:9: warning: unused variable 'fileList' [-Wunused-variable]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const':
pwiz/data/msdata/SpectrumIterator.cpp:126:58: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp:127:72: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:142:48: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const':
pwiz/utility/misc/IntegerSet.cpp:308:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
pwiz/utility/misc/IterationListener.cpp: In member function 'pwiz::util::IterationListener::Status pwiz::util::IterationListenerRegistry::Impl::broadcastUpdateMessage(const pwiz::util::IterationListener::UpdateMessage&) const':
pwiz/utility/misc/IterationListener.cpp:76:94: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
pwiz/utility/misc/IterationListener.cpp:78:87: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
pwiz/utility/misc/Filesystem.cpp:36:0: warning: "_WIN32_WINNT" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/_mingw.h:244:0: note: this is the location of the previous definition
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c random_access_gzFile.cpp -o random_access_gzFile.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -I. -DHAVE_PWIZ_MZML_LIB -I"E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c rampR.cpp -o rampR.o
g++ -m64 -shared -s -static-libgcc -o mzR.dll tmp.def cramp.o ramp_base64.o ramp.o RcppRamp.o RcppRampModule.o rnetCDF.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 ./pwiz/data/msdata/Version.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./boost/iostreams/src/zlib.o ./boost/filesystem/src/operations.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/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/ramp/wglob.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/SpectrumListCache.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 E:/biocbld/bbs-2.10-bioc/R/library/Rcpp/lib/x64/libRcpp.a -L./win//x64 -lws2_32 -lnetcdf -lz -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.10-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/mzR.buildbin-libdir/mzR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mzR' as mzR_1.2.2.zip
* DONE (mzR)