Steffen Neumann
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/mzR |
| git_branch: master |
| git_last_commit: 458704d6 |
| git_last_commit_date: 2022-01-25 11:51:47 -0400 (Tue, 25 Jan 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:08 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the mzR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mzR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1268/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mzR 2.29.3 (landing page) Steffen Neumann
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: mzR |
| Version: 2.29.3 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mzR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mzR_2.29.3.tar.gz |
| StartedAt: 2022-03-17 19:42:35 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:45:09 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 154.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mzR.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mzR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings mzR_2.29.3.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/mzR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-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 '2.29.3'
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
src/boost/serialization/collection_size_type copy.hpp
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'mzR' can be installed ... WARNING
Found the following significant warnings:
RcppPwiz.cpp:774:29: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
pwiz/data/msdata/MSData.cpp:1086:20: warning: control reaches end of non-void function [-Wreturn-type]
pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=]
pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder]
pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning: 'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder]
pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning: when initialized here [-Wreorder]
pwiz/data/proteome/Modification.cpp:89:5: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
pwiz/utility/minimxml/SAXParser.cpp:463:20: warning: offset '1' outside bounds of constant string [-Warray-bounds]
pwiz/utility/misc/Filesystem.cpp:156:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
pwiz/utility/misc/Filesystem.cpp:238:65: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
pwiz/utility/misc/Filesystem.cpp:251:146: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
pwiz/utility/misc/Filesystem.cpp:262:112: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
pwiz/utility/misc/Filesystem.cpp:269:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
See 'D:/biocbuild/bbs-3.15-bioc/meat/mzR.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 10.7Mb
sub-directories of 1Mb or more:
libs 10.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'Rhdf5lib' is only usable in R >= 3.0.2
* 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 ... OK
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
-fpermissive
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/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)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 5 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/mzR.Rcheck/00check.log'
for details.
mzR.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL mzR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'mzR' ...
** using staged installation
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture
rm -f RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./boost_aux/libs/nowide/src/iostream.o ./boost_aux/libs/nowide/src/cstdio.o ./boost_aux/libs/nowide/src/filebuf.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppPwiz.cpp -o RcppPwiz.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:29,
from RcppPwiz.h:12,
from RcppPwiz.cpp:1:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/MSDataFile.hpp:29,
from RcppPwiz.h:12,
from RcppPwiz.cpp:1:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:30,
from RcppPwiz.h:12,
from RcppPwiz.cpp:1:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp: In member function 'Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)':
RcppPwiz.cpp:406:44: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
if (current_scan < 1 || current_scan > n_scans) {
~~~~~~~~~~~~~^~~~~~~~~
RcppPwiz.cpp: In member function 'void RcppPwiz::addSpectrumList(pwiz::msdata::MSData&, Rcpp::DataFrame&, Rcpp::List&, bool)':
RcppPwiz.cpp:774:29: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
if (precursorScanNum[i] > 0 | precursorMZ[i] > 0) {
RcppPwiz.cpp: In member function 'Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)':
RcppPwiz.cpp:849:49: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
} else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
~~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:859:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::msdata::TimeIntensityPair>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i = 0; i < pairs.size(); i++) {
~~^~~~~~~~~~~~~~
RcppPwiz.cpp: In member function 'Rcpp::NumericMatrix RcppPwiz::get3DMap(std::vector<int>, double, double, double)':
RcppPwiz.cpp:1010:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i = 0; i < scanNumbers.size(); i++)
~~^~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp:1016:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::msdata::MZIntensityPair>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int k=0; k < pairs.size(); k++)
~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:29,
from RcppPwiz.h:12,
from RcppPwizModule.cpp:2:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/MSDataFile.hpp:29,
from RcppPwiz.h:12,
from RcppPwizModule.cpp:2:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:30,
from RcppPwiz.h:12,
from RcppPwizModule.cpp:2:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppIdent.cpp -o RcppIdent.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IdentDataFile.hpp:29,
from RcppIdent.h:11,
from RcppIdent.cpp:1:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
RcppIdent.cpp: In member function 'Rcpp::DataFrame RcppIdent::getScore()':
RcppIdent.cpp:293:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
for (size_t j = 0; j < nCvParams; j++) {
~~^~~~~~~~~~~
RcppIdent.cpp: In member function 'Rcpp::List RcppIdent::getPara()':
RcppIdent.cpp:382:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::data::CVParam>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++)
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RcppIdent.cpp:388:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<pwiz::data::UserParam>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppIdentModule.cpp -o RcppIdentModule.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IdentDataFile.hpp:29,
from RcppIdent.h:11,
from RcppIdentModule.cpp:2:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
In file included from ./boost/config.hpp:57,
from ./boost/system/config.hpp:13,
from boost/libs/system/src/error_code.cpp:17:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
In file included from ./boost/config.hpp:57,
from boost/libs/regex/src/posix_api.cpp:21:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
In file included from ./boost/config.hpp:57,
from ./boost/regex/config.hpp:76,
from boost/libs/regex/src/regex_debug.cpp:22:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
In file included from ./boost/config.hpp:57,
from ./boost/regex/config.hpp:76,
from boost/libs/regex/src/regex.cpp:22:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
In file included from ./boost/config.hpp:57,
from ./boost/regex/config.hpp:76,
from boost/libs/regex/src/wide_posix_api.cpp:21:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
In file included from ./boost/config.hpp:57,
from ./boost/regex/config.hpp:76,
from boost/libs/regex/src/static_mutex.cpp:20:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
In file included from ./boost/config.hpp:57,
from ./boost/exception/exception.hpp:9,
from ./boost/throw_exception.hpp:23,
from boost/libs/iostreams/src/zlib.cpp:17:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
In file included from ./boost/config.hpp:57,
from boost/libs/iostreams/src/file_descriptor.cpp:16:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/filesystem/src/platform_config.hpp:74,
from boost/libs/filesystem/src/operations.cpp:14:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/filesystem/src/platform_config.hpp:74,
from boost/libs/filesystem/src/directory.cpp:14:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/filesystem/src/platform_config.hpp:74,
from boost/libs/filesystem/src/exception.cpp:11:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/filesystem/src/platform_config.hpp:74,
from boost/libs/filesystem/src/path.cpp:10:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/filesystem/src/platform_config.hpp:74,
from boost/libs/filesystem/src/unique_path.cpp:13:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/filesystem/src/platform_config.hpp:74,
from boost/libs/filesystem/src/utf8_codecvt_facet.cpp:6:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
In file included from ./boost/config.hpp:57,
from ./boost/chrono/config.hpp:15,
from ./boost/chrono/duration.hpp:33,
from ./boost/chrono/chrono.hpp:11,
from ./boost/chrono/detail/inlined/chrono.hpp:13,
from boost/libs/chrono/src/chrono.cpp:14:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
In file included from ./boost/config.hpp:57,
from ./boost/chrono/config.hpp:15,
from ./boost/chrono/detail/inlined/process_cpu_clocks.hpp:15,
from boost/libs/chrono/src/process_cpu_clocks.cpp:17:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
In file included from ./boost/config.hpp:57,
from ./boost/chrono/config.hpp:15,
from ./boost/chrono/detail/inlined/thread_clock.hpp:14,
from boost/libs/chrono/src/thread_clock.cpp:18:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
In file included from ./boost/config.hpp:57,
from ./boost/iostreams/positioning.hpp:18,
from pwiz/data/common/Index.hpp:29,
from pwiz/data/common/MemoryIndex.hpp:26,
from pwiz/data/common/MemoryIndex.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from ./boost/checked_delete.hpp:15,
from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27,
from ./boost/smart_ptr/detail/shared_count.hpp:27,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/data/common/Index.hpp:30,
from pwiz/data/common/MemoryIndex.hpp:26,
from pwiz/data/common/MemoryIndex.cpp:25:
./boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::MemoryIndex::Impl]':
./boost/smart_ptr/detail/shared_count.hpp:154:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::MemoryIndex::Impl]'
./boost/smart_ptr/shared_ptr.hpp:279:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::MemoryIndex::Impl; Y = pwiz::data::MemoryIndex::Impl]'
./boost/smart_ptr/shared_ptr.hpp:373:44: required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::MemoryIndex::Impl; T = pwiz::data::MemoryIndex::Impl]'
pwiz/data/common/MemoryIndex.cpp:73:58: required from here
./boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type 'pwiz::data::MemoryIndex::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete x;
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/data/common/CVTranslator.hpp:31,
from pwiz/data/common/CVTranslator.cpp:27:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const string&, pwiz::cv::CVID, pwiz::cv::CVID)':
pwiz/data/common/CVTranslator.cpp:133:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:135:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:136:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/common/cv.cpp:34:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/common/cv.cpp:25029:
pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)':
pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'long long unsigned int' [-Wsign-compare]
for (int o=0;o<oboPrefixesSize_;++o)
~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/common/ParamTypes.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/config.hpp:57,
from ./boost/iostreams/positioning.hpp:18,
from pwiz/data/common/Index.hpp:29,
from pwiz/data/common/BinaryIndexStream.hpp:26,
from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from ./boost/checked_delete.hpp:15,
from ./boost/smart_ptr/detail/sp_counted_impl.hpp:27,
from ./boost/smart_ptr/detail/shared_count.hpp:27,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/data/common/Index.hpp:30,
from pwiz/data/common/BinaryIndexStream.hpp:26,
from pwiz/data/common/BinaryIndexStream.cpp:25:
./boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = pwiz::data::BinaryIndexStream::Impl]':
./boost/smart_ptr/detail/shared_count.hpp:154:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/smart_ptr/shared_ptr.hpp:279:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr<X>*, Y*, boost::detail::shared_count&) [with T = pwiz::data::BinaryIndexStream::Impl; Y = pwiz::data::BinaryIndexStream::Impl]'
./boost/smart_ptr/shared_ptr.hpp:373:44: required from 'boost::shared_ptr<T>::shared_ptr(Y*) [with Y = pwiz::data::BinaryIndexStream::Impl; T = pwiz::data::BinaryIndexStream::Impl]'
pwiz/data/common/BinaryIndexStream.cpp:417:103: required from here
./boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type 'pwiz::data::BinaryIndexStream::Impl' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
delete x;
^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/common/diff_std.hpp:33,
from pwiz/data/common/diff_std.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/common/Unimod.hpp:28,
from pwiz/data/common/Unimod.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:29,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:27,
from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/mz5/../MSData.hpp:30,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:27,
from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:28,
from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:29,
from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32,
from pwiz/data/msdata/mz5/Datastructures_mz5.cpp:25:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:28,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:29,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/data/msdata/mz5/../../common/ParamTypes.hpp:29,
from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:28,
from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/mz5/../MSData.hpp:29,
from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:29,
from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32,
from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/msdata/DefaultReaderList.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Reader.hpp:30,
from pwiz/data/msdata/DefaultReaderList.hpp:29,
from pwiz/data/msdata/DefaultReaderList.cpp:29:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/msdata/DefaultReaderList.hpp:29,
from pwiz/data/msdata/DefaultReaderList.cpp:29:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/ChromatogramListBase.hpp:28,
from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/ChromatogramListBase.hpp:28,
from pwiz/data/msdata/ChromatogramList_mzML.hpp:29,
from pwiz/data/msdata/ChromatogramList_mzML.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/References.hpp:29,
from pwiz/data/msdata/ChromatogramList_mz5.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31,
from pwiz/data/msdata/ChromatogramList_mz5.hpp:31,
from pwiz/data/msdata/ChromatogramList_mz5.cpp:28:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/examples.hpp:29,
from pwiz/data/msdata/examples.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/examples.hpp:29,
from pwiz/data/msdata/examples.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_mzML.hpp:29,
from pwiz/data/msdata/Serializer_mzML.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/Serializer_mzML.hpp:29,
from pwiz/data/msdata/Serializer_mzML.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_MSn.hpp:26,
from pwiz/data/msdata/Serializer_MSn.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/Serializer_MSn.hpp:26,
from pwiz/data/msdata/Serializer_MSn.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/misc/IterationListener.hpp:29,
from pwiz/data/msdata/Reader.hpp:28,
from pwiz/data/msdata/Reader.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Reader.hpp:30,
from pwiz/data/msdata/Reader.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/msdata/Reader.cpp:26:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/msdata/Serializer_mz5.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/References.hpp:29,
from pwiz/data/msdata/Serializer_mz5.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/Serializer_mz5.hpp:32,
from pwiz/data/msdata/Serializer_mz5.cpp:28:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_MGF.hpp:27,
from pwiz/data/msdata/Serializer_MGF.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/Serializer_MGF.hpp:27,
from pwiz/data/msdata/Serializer_MGF.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_mzXML.hpp:29,
from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/Serializer_mzXML.hpp:29,
from pwiz/data/msdata/Serializer_mzXML.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumListBase.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumListBase.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
from pwiz/data/msdata/SpectrumList_MGF.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/SpectrumList_mzML.cpp:31:
./boost/bind.hpp:41:1: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
)
^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
from pwiz/data/msdata/SpectrumList_MSn.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/References.hpp:29,
from pwiz/data/msdata/SpectrumList_mz5.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31,
from pwiz/data/msdata/SpectrumList_mz5.hpp:31,
from pwiz/data/msdata/SpectrumList_mz5.cpp:28:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
In file included from pwiz/data/msdata/BinaryDataEncoder.hpp:29,
from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/data/msdata/BinaryDataEncoder.hpp:30,
from pwiz/data/msdata/BinaryDataEncoder.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::__cxx11::string&, size_t*)':
pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteCount' may be used uninitialized in this function [-Wmaybe-uninitialized]
filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteBuffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Diff.hpp:29,
from pwiz/data/msdata/Diff.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/Diff.hpp:29,
from pwiz/data/msdata/Diff.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/MSData.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/MSData.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const string&, char) const':
pwiz/data/msdata/MSData.cpp:1086:20: warning: control reaches end of non-void function [-Wreturn-type]
vector<string> abbreviatedTokens, actualTokens;
^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/References.hpp:29,
from pwiz/data/msdata/References.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/References.hpp:29,
from pwiz/data/msdata/References.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
from pwiz/data/msdata/SpectrumList_mzXML.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr<std::basic_istream<char> >, const pwiz::msdata::MSData&, bool)':
pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=]
} catch (index_not_found e){
^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/IO.hpp:29,
from pwiz/data/msdata/IO.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/IO.hpp:29,
from pwiz/data/msdata/IO.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeBinaryDataArray(pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&)':
pwiz/data/msdata/IO.cpp:1657:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (usedConfig.byteOrder == BinaryDataEncoder::ByteOrder_BigEndian)
^~
pwiz/data/msdata/IO.cpp:1660:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
bool zlib = false; // Handle numpress+zlib
^~~~
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2132:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList")
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)':
pwiz/data/msdata/IO.cpp:2836:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from ./pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/SpectrumListBase.hpp:28,
from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
from pwiz/data/msdata/SpectrumList_BTDX.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumInfo.hpp:29,
from pwiz/data/msdata/SpectrumInfo.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/SpectrumInfo.hpp:29,
from pwiz/data/msdata/SpectrumInfo.cpp:27:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/LegacyAdapter.hpp:30,
from pwiz/data/msdata/LegacyAdapter.cpp:27:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/LegacyAdapter.hpp:30,
from pwiz/data/msdata/LegacyAdapter.cpp:27:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumIterator.hpp:29,
from pwiz/data/msdata/SpectrumIterator.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/SpectrumIterator.hpp:29,
from pwiz/data/msdata/SpectrumIterator.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
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:125:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
return (done() && &that.spectrumList_==&pastEndMarker_ ||
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
&spectrumList_==&that.spectrumList_ && currentIndex_==that.currentIndex_);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp: In member function 'bool pwiz::msdata::SpectrumIterator::Impl::done() const':
pwiz/data/msdata/SpectrumIterator.cpp:141:34: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:29,
from pwiz/data/msdata/MSDataFile.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/MSDataFile.hpp:29,
from pwiz/data/msdata/MSDataFile.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:30,
from pwiz/data/msdata/MSDataFile.cpp:26:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const':
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)':
pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
} else if (init == mask) {
~~~~~^~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListCache.hpp:27,
from pwiz/data/msdata/SpectrumListCache.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/SpectrumListCache.hpp:27,
from pwiz/data/msdata/SpectrumListCache.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
In file included from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Index_mzML.hpp:28,
from pwiz/data/msdata/Index_mzML.cpp:24:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/data/common/ParamTypes.hpp:29,
from pwiz/data/msdata/MSData.hpp:30,
from pwiz/data/msdata/Index_mzML.hpp:28,
from pwiz/data/msdata/Index_mzML.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from ./pwiz/data/msdata/SpectrumWorkerThreads.hpp:26,
from pwiz/data/msdata/SpectrumWorkerThreads.cpp:26:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IdentDataFile.hpp:29,
from pwiz/data/identdata/IdentDataFile.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/identdata/IdentData.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/identdata/DefaultReaderList.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Reader.hpp:28,
from pwiz/data/identdata/Reader.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Serializer_protXML.hpp:29,
from pwiz/data/identdata/Serializer_protXML.cpp:28:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/identdata/Serializer_protXML.cpp:36:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
pwiz/data/identdata/Serializer_protXML.cpp: In constructor 'pwiz::identdata::{anonymous}::Handler_protXML::Handler_protXML(pwiz::identdata::IdentData&, const pwiz::util::IterationListenerRegistry*, bool, std::vector<std::__cxx11::basic_string<char> >*)':
pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: 'pwiz::identdata::{anonymous}::Handler_protXML::strict' will be initialized after [-Wreorder]
bool strict;
^~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning: 'int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides' [-Wreorder]
int nPeptides;
^~~~~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning: when initialized here [-Wreorder]
Handler_protXML(IdentData& mzid,
^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Serializer_pepXML.hpp:27,
from pwiz/data/identdata/Serializer_pepXML.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/identdata/Serializer_pepXML.cpp:33:
./pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
./pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
./pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
./pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
./pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
./pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
./pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
pwiz/data/identdata/Serializer_pepXML.cpp: In function 'void pwiz::identdata::{anonymous}::write_spectrum_queries(pwiz::minimxml::XMLWriter&, const pwiz::identdata::IdentData&, const string&, const pwiz::util::IterationListenerRegistry*)':
pwiz/data/identdata/Serializer_pepXML.cpp:801:52: warning: 'lastSpectrumIndex' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/Serializer_mzid.hpp:28,
from pwiz/data/identdata/Serializer_mzid.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/IO.hpp:27,
from pwiz/data/identdata/IO.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from ./pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/identdata/IdentData.hpp:30,
from pwiz/data/identdata/References.hpp:29,
from pwiz/data/identdata/References.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/data/identdata/References.cpp: In function 'void pwiz::identdata::References::resolve(std::vector<boost::shared_ptr<pwiz::identdata::Contact> >&, pwiz::identdata::IdentData&)':
pwiz/data/identdata/References.cpp:148:17: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
else if (dynamic_cast<Person*>(c.get()))
^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/data/identdata/MascotReader.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Peptide.hpp:29,
from pwiz/data/proteome/Modification.hpp:30,
from pwiz/data/proteome/Modification.cpp:27:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/data/proteome/Modification.cpp:89:5: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
auto_ptr<Formula> formula_;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from ./boost/smart_ptr/detail/shared_count.hpp:27,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Peptide.hpp:29,
from pwiz/data/proteome/Modification.hpp:30,
from pwiz/data/proteome/Modification.cpp:27:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Digestion.hpp:31,
from pwiz/data/proteome/Digestion.cpp:27:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/Peptide.hpp:29,
from pwiz/data/proteome/Peptide.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from ./pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/data/proteome/AminoAcid.hpp:29,
from pwiz/data/proteome/AminoAcid.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/utility/minimxml/XMLWriter.hpp:29,
from pwiz/utility/minimxml/XMLWriter.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/utility/minimxml/SAXParser.hpp:31,
from pwiz/utility/minimxml/SAXParser.cpp:28:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, pwiz::minimxml::SAXParser::Handler&)':
pwiz/utility/minimxml/SAXParser.cpp:463:20: warning: offset '1' outside bounds of constant string [-Warray-bounds]
PWIZ_API_DECL void parse(istream& is, Handler& handler)
^~~~~
pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (inCDATA)
^~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/utility/chemistry/Chemistry.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/chemistry/Chemistry.hpp:33,
from pwiz/utility/chemistry/ChemistryData.hpp:29,
from pwiz/utility/chemistry/ChemistryData.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/chemistry/MZTolerance.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/misc/IntegerSet.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
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:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from ./pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/misc/Base64.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o
In file included from pwiz/utility/misc/BinaryData.cpp:24:
pwiz/utility/misc/BinaryData.hpp:124: warning: ignoring #pragma region Ctors [-Wunknown-pragmas]
#pragma region Ctors/Dtor
pwiz/utility/misc/BinaryData.hpp:136: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
pwiz/utility/misc/BinaryData.hpp:138: warning: ignoring #pragma region Iterators [-Wunknown-pragmas]
#pragma region Iterators/accessors
pwiz/utility/misc/BinaryData.hpp:267: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
pwiz/utility/misc/BinaryData.hpp:269: warning: ignoring #pragma region Mutators [-Wunknown-pragmas]
#pragma region Mutators
pwiz/utility/misc/BinaryData.hpp:377: warning: ignoring #pragma endregion [-Wunknown-pragmas]
#pragma endregion
pwiz/utility/misc/BinaryData.hpp:389: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(push)
pwiz/utility/misc/BinaryData.hpp:390: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(disable: 4251)
pwiz/utility/misc/BinaryData.hpp:392: warning: ignoring #pragma warning [-Wunknown-pragmas]
#pragma warning(pop)
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from pwiz/utility/misc/BinaryData.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/utility/misc/BinaryData.cpp:302: warning: ignoring #pragma managed [-Wunknown-pragmas]
#pragma managed(push, off)
pwiz/utility/misc/BinaryData.cpp:474: warning: ignoring #pragma managed [-Wunknown-pragmas]
#pragma managed(pop)
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
In file included from ./boost/config.hpp:57,
from ./boost/lexical_cast.hpp:21,
from ./pwiz/utility/misc/optimized_lexical_cast.hpp:29,
from ./pwiz/utility/misc/Environment.hpp:24,
from pwiz/utility/misc/Std.hpp:29,
from pwiz/utility/misc/IterationListener.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/misc/TabReader.hpp:29,
from pwiz/utility/misc/MSIHandler.hpp:28,
from pwiz/utility/misc/MSIHandler.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
In file included from ./boost/config.hpp:57,
from ./boost/algorithm/string/std_containers_traits.hpp:18,
from ./boost/algorithm/string.hpp:18,
from pwiz/utility/misc/String.hpp:31,
from pwiz/utility/misc/Filesystem.hpp:34,
from pwiz/utility/misc/Filesystem.cpp:26:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
pwiz/utility/misc/Filesystem.cpp:29: warning: "_WIN32_WINNT" redefined
#define _WIN32_WINNT 0x0600
In file included from C:/rtools40/mingw64/x86_64-w64-mingw32/include/crtdefs.h:10,
from C:/rtools40/mingw64/x86_64-w64-mingw32/include/wchar.h:9,
from C:/rtools40/mingw64/include/c++/8.3.0/cwchar:44,
from C:/rtools40/mingw64/include/c++/8.3.0/bits/postypes.h:40,
from C:/rtools40/mingw64/include/c++/8.3.0/bits/char_traits.h:40,
from C:/rtools40/mingw64/include/c++/8.3.0/string:40,
from pwiz/utility/misc/String.hpp:27,
from pwiz/utility/misc/Filesystem.hpp:34,
from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/_mingw.h:225: note: this is the location of the previous definition
#define _WIN32_WINNT 0x502
pwiz/utility/misc/Filesystem.cpp:31: warning: "NOMINMAX" redefined
#define NOMINMAX
In file included from C:/rtools40/mingw64/include/c++/8.3.0/x86_64-w64-mingw32/bits/c++config.h:508,
from C:/rtools40/mingw64/include/c++/8.3.0/string:38,
from pwiz/utility/misc/String.hpp:27,
from pwiz/utility/misc/Filesystem.hpp:34,
from pwiz/utility/misc/Filesystem.cpp:26:
C:/rtools40/mingw64/include/c++/8.3.0/x86_64-w64-mingw32/bits/os_defines.h:45: note: this is the location of the previous definition
#define NOMINMAX 1
pwiz/utility/misc/Filesystem.cpp: In function 'void* {anonymous}::GetLibraryProcAddress(PSTR, PSTR)':
pwiz/utility/misc/Filesystem.cpp:141:30: warning: invalid conversion from 'FARPROC' {aka 'long long int (*)()'} to 'PVOID' {aka 'void*'} [-fpermissive]
return GetProcAddress(GetModuleHandleA(LibraryName), ProcName);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp: In function 'int {anonymous}::GetFileHandleTypeNumber(SYSTEM_HANDLE_INFORMATION*)':
pwiz/utility/misc/Filesystem.cpp:156:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
_NtQueryObject NtQueryObject = (_NtQueryObject)GetLibraryProcAddress("ntdll.dll", "NtQueryObject");
^
pwiz/utility/misc/Filesystem.cpp:156:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
pwiz/utility/misc/Filesystem.cpp:175:29: warning: comparison of integer expressions of different signedness: 'long int' and 'unsigned int' [-Wsign-compare]
if (queryResult == STATUS_INFO_LENGTH_MISMATCH)
^
pwiz/utility/misc/Filesystem.cpp: In function 'bool pwiz::util::running_on_wine()':
pwiz/utility/misc/Filesystem.cpp:238:65: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
return GetLibraryProcAddress("ntdll.dll", "wine_get_version") != NULL;
^
pwiz/utility/misc/Filesystem.cpp:238:65: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const string&, bool)':
pwiz/utility/misc/Filesystem.cpp:251:146: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
_NtQuerySystemInformation NtQuerySystemInformation = (_NtQuerySystemInformation)GetLibraryProcAddress("ntdll.dll", "NtQuerySystemInformation");
^
pwiz/utility/misc/Filesystem.cpp:251:146: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
pwiz/utility/misc/Filesystem.cpp:262:112: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
NtUnmapViewOfSection = (_NtUnmapViewOfSection)GetLibraryProcAddress("ntdll.dll", "NtUnmapViewOfSection");
^
pwiz/utility/misc/Filesystem.cpp:262:112: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
pwiz/utility/misc/Filesystem.cpp:269:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
NtMapViewOfSection = (_NtMapViewOfSection)GetLibraryProcAddress("ntdll.dll", "NtMapViewOfSection");
^
pwiz/utility/misc/Filesystem.cpp:269:106: warning: ISO C++ forbids converting a string constant to 'PSTR' {aka 'char*'} [-Wwrite-strings]
pwiz/utility/misc/Filesystem.cpp:286:20: warning: comparison of integer expressions of different signedness: 'NTSTATUS' {aka 'long int'} and 'unsigned int' [-Wsign-compare]
if (status == STATUS_INFO_LENGTH_MISMATCH)
^
pwiz/utility/misc/Filesystem.cpp:294:21: warning: comparison of integer expressions of different signedness: 'NTSTATUS' {aka 'long int'} and 'unsigned int' [-Wsign-compare]
} while (status == STATUS_INFO_LENGTH_MISMATCH);
^
pwiz/utility/misc/Filesystem.cpp:372:59: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
if (!GetFileNameFromHandle((HANDLE)handleInfo.HandleValue, szPath, 260))
^~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:385:53: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
if (!CloseHandle((HANDLE)handleInfo.HandleValue))
^~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:397:69: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
NTSTATUS status = NtMapViewOfSection((HANDLE)handleInfo.HandleValue, currentProcessHandle, &viewBase, 0, 0, NULL, &viewSize, ViewShare, 0, PAGE_READONLY);
^~~~~~~~~~~
pwiz/utility/misc/Filesystem.cpp:413:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
if (!CloseHandle((HANDLE)handleInfo.HandleValue))
^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/misc/TabReader.hpp:29,
from pwiz/utility/misc/TabReader.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/config.hpp:57,
from ./boost/iostreams/positioning.hpp:18,
from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
In file included from ./boost/config.hpp:57,
from ./boost/static_assert.hpp:17,
from pwiz/utility/misc/endian.hpp:28,
from pwiz/utility/misc/SHA1.cpp:10:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
In file included from ./boost/config.hpp:57,
from ./boost/static_assert.hpp:17,
from pwiz/utility/misc/endian.hpp:28,
from pwiz/utility/misc/SHA1Calculator.cpp:25:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
In file included from ./boost/config.hpp:57,
from ./boost/smart_ptr/bad_weak_ptr.hpp:20,
from ./boost/smart_ptr/detail/shared_count.hpp:25,
from ./boost/smart_ptr/shared_ptr.hpp:17,
from ./boost/shared_ptr.hpp:17,
from pwiz/utility/misc/SHA1Calculator.hpp:28,
from pwiz/utility/misc/sha1calc.cpp:24:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o
In file included from ./boost/config.hpp:57,
from ./boost/algorithm/string/std_containers_traits.hpp:18,
from ./boost/algorithm/string.hpp:18,
from pwiz/utility/misc/String.hpp:31,
from pwiz/utility/misc/String.cpp:21:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/filesystem/src/platform_config.hpp:74,
from boost/libs/filesystem/src/path_traits.cpp:12:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/filesystem/src/platform_config.hpp:74,
from boost/libs/filesystem/src/windows_file_codecvt.cpp:12:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/filesystem/src/platform_config.hpp:74,
from boost/libs/filesystem/src/codecvt_error_category.cpp:12:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/thread/src/win32/tss_pe.cpp -o boost/libs/thread/src/win32/tss_pe.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/thread/src/win32/tss_pe.cpp:10:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/thread/src/win32/tss_dll.cpp -o boost/libs/thread/src/win32/tss_dll.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/thread/src/win32/tss_dll.cpp:6:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost/libs/thread/src/win32/thread.cpp -o boost/libs/thread/src/win32/thread.o
In file included from ./boost/config.hpp:57,
from ./boost/winapi/config.hpp:235,
from boost/libs/thread/src/win32/thread.cpp:10:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost_aux/libs/nowide/src/iostream.cpp -o boost_aux/libs/nowide/src/iostream.o
In file included from ./boost/config.hpp:57,
from ./boost/nowide/config.hpp:14,
from ./boost/nowide/iostream.hpp:12,
from boost_aux/libs/nowide/src/iostream.cpp:9:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
boost_aux/libs/nowide/src/iostream.cpp: In member function 'virtual int boost::nowide::detail::console_input_buffer::underflow()':
boost_aux/libs/nowide/src/iostream.cpp:189:13: warning: 'c' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(c==uf::incomplete) {
^~
boost_aux/libs/nowide/src/iostream.cpp:178:28: note: 'c' was declared here
uf::code_point c;
^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost_aux/libs/nowide/src/cstdio.cpp -o boost_aux/libs/nowide/src/cstdio.o
In file included from ./boost/config.hpp:57,
from ./boost/nowide/config.hpp:14,
from ./boost/nowide/cstdio.hpp:12,
from boost_aux/libs/nowide/src/cstdio.cpp:19:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c boost_aux/libs/nowide/src/filebuf.cpp -o boost_aux/libs/nowide/src/filebuf.o
boost_aux/libs/nowide/src/filebuf.cpp:23: warning: "_LARGEFILE_SOURCE" redefined
#define _LARGEFILE_SOURCE
<command-line>: note: this is the location of the previous definition
In file included from ./boost/config.hpp:57,
from ./boost/nowide/config.hpp:14,
from ./boost/nowide/filebuf.hpp:12,
from boost_aux/libs/nowide/src/filebuf.cpp:34:
./boost/config/platform/win32.hpp:61: warning: "BOOST_HAS_WINTHREADS" redefined
# define BOOST_HAS_WINTHREADS
<command-line>: note: this is the location of the previous definition
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o mzR.dll tmp.def RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o ./boost/libs/regex/src/posix_api.o ./boost/libs/regex/src/regex_debug.o ./boost/libs/regex/src/regex.o ./boost/libs/regex/src/wide_posix_api.o ./boost/libs/regex/src/static_mutex.o ./boost/libs/iostreams/src/zlib.o ./boost/libs/iostreams/src/file_descriptor.o ./boost/libs/filesystem/src/operations.o ./boost/libs/filesystem/src/directory.o ./boost/libs/filesystem/src/exception.o ./boost/libs/filesystem/src/path.o ./boost/libs/filesystem/src/unique_path.o ./boost/libs/filesystem/src/utf8_codecvt_facet.o ./boost/libs/chrono/src/chrono.o ./boost/libs/chrono/src/process_cpu_clocks.o ./boost/libs/chrono/src/thread_clock.o ./pwiz/data/msdata/Version.o ./pwiz/data/identdata/Version.o ./pwiz/data/common/MemoryIndex.o ./pwiz/data/common/CVTranslator.o ./pwiz/data/common/cv.o ./pwiz/data/common/ParamTypes.o ./pwiz/data/common/BinaryIndexStream.o ./pwiz/data/common/diff_std.o ./pwiz/data/common/Unimod.o ./pwiz/data/msdata/mz5/Configuration_mz5.o ./pwiz/data/msdata/mz5/Connection_mz5.o ./pwiz/data/msdata/mz5/Datastructures_mz5.o ./pwiz/data/msdata/mz5/ReferenceRead_mz5.o ./pwiz/data/msdata/mz5/ReferenceWrite_mz5.o ./pwiz/data/msdata/mz5/Translator_mz5.o ./pwiz/data/msdata/DefaultReaderList.o ./pwiz/data/msdata/ChromatogramList_mzML.o ./pwiz/data/msdata/ChromatogramList_mz5.o ./pwiz/data/msdata/examples.o ./pwiz/data/msdata/Serializer_mzML.o ./pwiz/data/msdata/Serializer_MSn.o ./pwiz/data/msdata/Reader.o ./pwiz/data/msdata/Serializer_mz5.o ./pwiz/data/msdata/Serializer_MGF.o ./pwiz/data/msdata/Serializer_mzXML.o ./pwiz/data/msdata/SpectrumListBase.o ./pwiz/data/msdata/SpectrumList_MGF.o ./pwiz/data/msdata/SpectrumList_mzML.o ./pwiz/data/msdata/SpectrumList_MSn.o ./pwiz/data/msdata/SpectrumList_mz5.o ./pwiz/data/msdata/BinaryDataEncoder.o ./pwiz/data/msdata/Diff.o ./pwiz/data/msdata/MSData.o ./pwiz/data/msdata/References.o ./pwiz/data/msdata/SpectrumList_mzXML.o ./pwiz/data/msdata/IO.o ./pwiz/data/msdata/SpectrumList_BTDX.o ./pwiz/data/msdata/SpectrumInfo.o ./pwiz/data/msdata/LegacyAdapter.o ./pwiz/data/msdata/SpectrumIterator.o ./pwiz/data/msdata/MSDataFile.o ./pwiz/data/msdata/MSNumpress.o ./pwiz/data/msdata/SpectrumListCache.o ./pwiz/data/msdata/Index_mzML.o ./pwiz/data/msdata/SpectrumWorkerThreads.o ./pwiz/data/identdata/IdentDataFile.o ./pwiz/data/identdata/IdentData.o ./pwiz/data/identdata/DefaultReaderList.o ./pwiz/data/identdata/Reader.o ./pwiz/data/identdata/Serializer_protXML.o ./pwiz/data/identdata/Serializer_pepXML.o ./pwiz/data/identdata/Serializer_mzid.o ./pwiz/data/identdata/IO.o ./pwiz/data/identdata/References.o ./pwiz/data/identdata/MascotReader.o ./pwiz/data/proteome/Modification.o ./pwiz/data/proteome/Digestion.o ./pwiz/data/proteome/Peptide.o ./pwiz/data/proteome/AminoAcid.o ./pwiz/utility/minimxml/XMLWriter.o ./pwiz/utility/minimxml/SAXParser.o ./pwiz/utility/chemistry/Chemistry.o ./pwiz/utility/chemistry/ChemistryData.o ./pwiz/utility/chemistry/MZTolerance.o ./pwiz/utility/misc/IntegerSet.o ./pwiz/utility/misc/Base64.o ./pwiz/utility/misc/BinaryData.o ./pwiz/utility/misc/IterationListener.o ./pwiz/utility/misc/MSIHandler.o ./pwiz/utility/misc/Filesystem.o ./pwiz/utility/misc/TabReader.o ./pwiz/utility/misc/random_access_compressed_ifstream.o ./pwiz/utility/misc/SHA1.o ./pwiz/utility/misc/SHA1Calculator.o ./pwiz/utility/misc/sha1calc.o ./pwiz/utility/misc/String.o ./RcppExports.o ./boost/libs/filesystem/src/path_traits.o ./boost/libs/filesystem/src/windows_file_codecvt.o ./boost/libs/filesystem/src/codecvt_error_category.o ./boost/libs/thread/src/win32/tss_pe.o ./boost/libs/thread/src/win32/tss_dll.o ./boost/libs/thread/src/win32/thread.o ./boost_aux/libs/nowide/src/iostream.o ./boost_aux/libs/nowide/src/cstdio.o ./boost_aux/libs/nowide/src/filebuf.o -lpthread -LD:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -lws2_32 -lz -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-mzR/00new/mzR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mzR'
finding HTML links ... done
copyWriteMSData html
isolationWindow-methods html
metadata html
mzR-class html
finding level-2 HTML links ... done
openMSfile html
peaks html
pwiz-version html
writeMSData html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mzR)
Making 'packages.html' ... done
mzR.Rcheck/tests/runTests.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("mzR")
Loading required package: Rcpp
> library("msdata")
>
>
> ## Catch warnings as well:
> #options(warn = 2)
>
> BiocGenerics:::testPackage("mzR")
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x) : attempt to apply non-function
Loading required namespace: XML
reading Tandem.mzid.gz... DONE!
Mass Spectrometry file handle.
Filename: MM14.mzML
Number of scans: 112
Mass Spectrometry file handle.
Filename: threonine_i2_e35_pH_tree.mzXML
Number of scans: 55
RUNIT TEST PROTOCOL -- Thu Mar 17 19:45:00 2022
***********************************************
Number of test functions: 28
Number of errors: 0
Number of failures: 0
1 Test Suite :
mzR RUnit Tests - 28 test functions, 0 errors, 0 failures
Number of test functions: 28
Number of errors: 0
Number of failures: 0
Warning messages:
1: pwiz not yet initialized.
2: pwiz not yet initialized.
>
> proc.time()
user system elapsed
27.12 5.06 35.14
mzR.Rcheck/mzR-Ex.timings
| name | user | system | elapsed | |
| copyWriteMSData | 0.11 | 0.00 | 0.11 | |
| isolationWindow-methods | 1.23 | 0.36 | 1.60 | |
| metadata | 0.66 | 0.52 | 1.28 | |
| mzR-class | 0.01 | 0.04 | 0.06 | |
| openMSfile | 0.41 | 0.49 | 0.89 | |
| peaks | 0.75 | 0.14 | 0.89 | |
| writeMSData | 0.06 | 0.00 | 0.06 | |