Rapid builds (Linux only) of a subset of BioC 3.23<BR>Report updated every 6 hours

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-06 r89561) -- "Unsuffered Consequences"	903
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*

CHECK results for mzR on teran2

To the developers/maintainers of the mzR package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: mzR

Version: 2.45.0

Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings mzR_2.45.0.tar.gz

StartedAt: 2026-03-12 15:04:51 -0400 (Thu, 12 Mar 2026)

EndedAt: 2026-03-12 15:05:58 -0400 (Thu, 12 Mar 2026)

EllapsedTime: 66.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: mzR.Rcheck

Warnings: 2

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings mzR_2.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/mzR.Rcheck’
* using R Under development (unstable) (2026-03-06 r89561)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* current time: 2026-03-12 19:04:53 UTC
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.45.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Steffen Neumann <sneumann@ipb-halle.de>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

The Title field should be in title case. Current version is:
  ‘parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)’
In title case that is:
  ‘Parser for netCDF, mzXML and mzML and mzIdentML Files (Mass Spectrometry Data)’

The Description field should not start with the package name,
  'This package' or similar.
* 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.

CRAN-pack does not know about
  .BBSoptions
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... WARNING
Found the following significant warnings:
  ./pwiz/utility/misc/BinaryData.hpp:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  ./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  RcppPwiz.cpp:414:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  RcppPwiz.cpp:885:55: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  ./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  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/TextWriter.hpp:887:46: warning: ignoring return value of ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator> std::operator+(const _CharT*, const __cxx11::basic_string<_CharT, _Traits, _Allocator>&) [with _CharT = char; _Traits = char_traits<char>; _Alloc = allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
  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: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  pwiz/utility/minimxml/SAXParser.cpp:543:61: warning: offset ‘1’ outside bounds of constant string [-Warray-bounds=]
  pwiz/utility/misc/BinaryData.hpp:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
Found the following additional notes/warnings:
  SystemRequirements specified C++11: support has been removed
See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/mzR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... NOTE
  Obsolete C++11 standard request will be ignored
* checking installed package size ... INFO
  installed size is 126.0Mb
  sub-directories of 1Mb or more:
    libs  125.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    ‘Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer’
  Authors@R: ‘Steffen Neumann [aut, cre], Laurent Gatto [aut], Qiakng Kou [aut], David Rauh [ctb], Sascha Manier [ctb], Adriano Rutz [ctb] (ORCID: <https://orcid.org/0000-0003-0443-9902>)’

* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mzR-class.Rd: Versioned-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* checking for GNU extensions in Makefiles ... INFO
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 ... WARNING
Note: information on .o files is not available
File ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/mzR/libs/mzR.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 nor [v]sprintf. 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/mzR.Rcheck/00check.log’
for details.

Installation output

mzR.Rcheck/00install.out

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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL mzR
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘mzR’ ...
** this is package ‘mzR’ version ‘2.45.0’
** using staged installation
** libs
specified C++11
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
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/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/bits/specfun.h:43,
                 from /usr/include/c++/13/cmath:3699,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:37,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include/Rcpp/r/headers.h:67,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include/RcppCommon.h:30,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include/Rcpp.h:27,
                 from RcppPwiz.h:4:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30:
./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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)’:
RcppPwiz.cpp:413:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  413 |       if (current_scan < 1 || current_scan > n_scans) {
      |                               ~~~~~~~~~~~~~^~~~~~~~~
RcppPwiz.cpp:414:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  414 |         Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans);
      |                                                       ~^       ~~~~~~~
      |                                                        |       |
      |                                                        int     size_t {aka long unsigned int}
      |                                                       %ld
RcppPwiz.cpp: In member function ‘Rcpp::DataFrame RcppPwiz::getChromatogramsInfo(int)’:
RcppPwiz.cpp:884:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  884 |     } else if ( (whichChrom < 1) || (whichChrom > clp->size()) ) {
      |                                      ~~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:885:55: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  885 |       Rprintf("Index whichChrom out of bounds [1 ... %d].\n", (clp->size()));
      |                                                      ~^       ~~~~~~~~~~~~~
      |                                                       |                 |
      |                                                       int               size_t {aka long unsigned int}
      |                                                      %ld
RcppPwiz.cpp:895:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::msdata::TimeIntensityPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  895 |       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:1047:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1047 |       for (int i = 0; i < scanNumbers.size(); i++)
      |                       ~~^~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp:1053:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::msdata::MZIntensityPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1053 |           for (int k=0; k < pairs.size(); k++)
      |                         ~~^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/bits/specfun.h:43,
                 from /usr/include/c++/13/cmath:3699,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include/Rcpp/platform/compiler.h:37,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include/Rcpp/r/headers.h:67,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include/RcppCommon.h:30,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include/Rcpp.h:27,
                 from RcppPwizModule.cpp:1:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30:
./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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppIdent.cpp -o RcppIdent.o
RcppIdent.cpp: In member function ‘Rcpp::DataFrame RcppIdent::getScore()’:
RcppIdent.cpp:293:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  293 |           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 unsigned int’} [-Wsign-compare]
  382 |     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 unsigned int’} [-Wsign-compare]
  388 |     for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppIdentModule.cpp -o RcppIdentModule.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
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*, 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:73:44:   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]
   36 |     delete x;
      |     ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
pwiz/data/common/CVTranslator.cpp: In function ‘bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)’:
pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  145 |     return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:147:40: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  147 |             key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
pwiz/data/common/CVTranslator.cpp:148:40: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  148 |             key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from pwiz/data/common/cv.cpp:27380:
pwiz/data/common/cv.inl: In function ‘const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)’:
pwiz/data/common/cv.inl:103:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  103 |         for (int o=0;o<oboPrefixesSize_;++o)
      |                      ~^~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/thread/thread_only.hpp:17,
                 from ./boost/thread/thread.hpp:12,
                 from pwiz/data/common/BinaryIndexStream.cpp:27:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
In file included from ./boost/functional/hash.hpp:6,
                 from ./boost/thread/detail/thread.hpp:41,
                 from ./boost/thread/thread_only.hpp:22:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from pwiz/data/common/Index.hpp:27,
                 from pwiz/data/common/BinaryIndexStream.hpp:26,
                 from pwiz/data/common/BinaryIndexStream.cpp:25:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
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:
./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*, 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:417:82:   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]
   36 |     delete x;
      |     ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
In file included from ./boost_aux/boost/enum.hpp:21,
                 from pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/common/Unimod.cpp:25:
pwiz/data/common/Unimod.hpp: In function ‘bool pwiz::data::unimod::operator==(const Site::domain&, const Site&)’:
./boost_aux/boost/enum/macros.hpp:226:85: warning: in C++20 this comparison calls the current function recursively with reversed arguments
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                                                                                 ~~~~^~~~~~
./boost_aux/boost/enum/macros.hpp:234:5: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
  234 |     BOOST_ENUM_DOMAIN_OPERATORS(_name) \
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp:69:1: note: in expansion of macro ‘BOOST_BITFIELD_DOMAIN_OPERATORS’
   69 | BOOST_BITFIELD_DOMAIN_OPERATORS(Site)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp: In function ‘bool pwiz::data::unimod::operator==(const Position::domain&, const Position&)’:
./boost_aux/boost/enum/macros.hpp:226:85: warning: in C++20 this comparison calls the current function recursively with reversed arguments
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                                                                                 ~~~~^~~~~~
pwiz/data/common/Unimod.hpp:78:1: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
   78 | BOOST_ENUM_DOMAIN_OPERATORS(Position)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp: In function ‘bool pwiz::data::unimod::operator==(const Classification::domain&, const Classification&)’:
./boost_aux/boost/enum/macros.hpp:226:85: warning: in C++20 this comparison calls the current function recursively with reversed arguments
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                                                                                 ~~~~^~~~~~
./boost_aux/boost/enum/macros.hpp:234:5: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
  234 |     BOOST_ENUM_DOMAIN_OPERATORS(_name) \
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp:97:1: note: in expansion of macro ‘BOOST_BITFIELD_DOMAIN_OPERATORS’
   97 | BOOST_BITFIELD_DOMAIN_OPERATORS(Classification)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp: In function ‘bool pwiz::data::unimod::operator==(const Site::domain&, const Site&)’:
./boost_aux/boost/enum/macros.hpp:226:17: warning: infinite recursion detected [-Winfinite-recursion]
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                 ^~~~~~~~
./boost_aux/boost/enum/macros.hpp:234:5: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
  234 |     BOOST_ENUM_DOMAIN_OPERATORS(_name) \
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp:69:1: note: in expansion of macro ‘BOOST_BITFIELD_DOMAIN_OPERATORS’
   69 | BOOST_BITFIELD_DOMAIN_OPERATORS(Site)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost_aux/boost/enum/macros.hpp:226:85: note: recursive call
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                                                                                 ~~~~^~~~~~
./boost_aux/boost/enum/macros.hpp:234:5: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
  234 |     BOOST_ENUM_DOMAIN_OPERATORS(_name) \
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp:69:1: note: in expansion of macro ‘BOOST_BITFIELD_DOMAIN_OPERATORS’
   69 | BOOST_BITFIELD_DOMAIN_OPERATORS(Site)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp: In function ‘bool pwiz::data::unimod::operator==(const Position::domain&, const Position&)’:
./boost_aux/boost/enum/macros.hpp:226:17: warning: infinite recursion detected [-Winfinite-recursion]
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                 ^~~~~~~~
pwiz/data/common/Unimod.hpp:78:1: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
   78 | BOOST_ENUM_DOMAIN_OPERATORS(Position)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost_aux/boost/enum/macros.hpp:226:85: note: recursive call
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                                                                                 ~~~~^~~~~~
pwiz/data/common/Unimod.hpp:78:1: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
   78 | BOOST_ENUM_DOMAIN_OPERATORS(Position)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp: In function ‘bool pwiz::data::unimod::operator==(const Classification::domain&, const Classification&)’:
./boost_aux/boost/enum/macros.hpp:226:17: warning: infinite recursion detected [-Winfinite-recursion]
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                 ^~~~~~~~
./boost_aux/boost/enum/macros.hpp:234:5: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
  234 |     BOOST_ENUM_DOMAIN_OPERATORS(_name) \
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp:97:1: note: in expansion of macro ‘BOOST_BITFIELD_DOMAIN_OPERATORS’
   97 | BOOST_BITFIELD_DOMAIN_OPERATORS(Classification)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./boost_aux/boost/enum/macros.hpp:226:85: note: recursive call
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                                                                                 ~~~~^~~~~~
./boost_aux/boost/enum/macros.hpp:234:5: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
  234 |     BOOST_ENUM_DOMAIN_OPERATORS(_name) \
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/common/Unimod.hpp:97:1: note: in expansion of macro ‘BOOST_BITFIELD_DOMAIN_OPERATORS’
   97 | BOOST_BITFIELD_DOMAIN_OPERATORS(Classification)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from pwiz/data/msdata/mz5/../../common/cv.hpp:35,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:27:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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:
./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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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:
./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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from pwiz/data/msdata/mz5/../../common/cv.hpp:35,
                 from pwiz/data/msdata/mz5/Datastructures_mz5.hpp:27:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from pwiz/data/msdata/mz5/../../common/cv.hpp:35,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:27:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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:
./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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/mz5/../SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/mz5/../SpectrumList_mz5.hpp:29,
                 from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:27:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from pwiz/data/msdata/mz5/../../common/cv.hpp:35,
                 from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:27:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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:
./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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:30:
./pwiz/utility/misc/BinaryData.hpp: At global scope:
./pwiz/utility/misc/BinaryData.hpp:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from ./pwiz/utility/misc/Std.hpp:28,
                 from pwiz/data/msdata/DefaultReaderList.cpp:26:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/DefaultReaderList.cpp:30:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o
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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from ./pwiz/utility/misc/Std.hpp:28,
                 from pwiz/data/msdata/ChromatogramList_mz5.cpp:26:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzML.cpp:28:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:29:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:30:
./pwiz/utility/misc/BinaryData.hpp: At global scope:
./pwiz/utility/misc/BinaryData.hpp:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/stl_tempbuf.h:61,
                 from /usr/include/c++/13/memory:66,
                 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/misc/IterationListener.hpp:29,
                 from pwiz/data/msdata/Reader.hpp:28:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o
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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from ./pwiz/utility/misc/Std.hpp:28,
                 from pwiz/data/msdata/Serializer_mz5.cpp:26:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mz5.hpp:29,
                 from pwiz/data/msdata/Serializer_mz5.cpp:29:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MGF.hpp:30,
                 from pwiz/data/msdata/Serializer_MGF.cpp:26:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mzXML.hpp:29,
                 from pwiz/data/msdata/Serializer_mzXML.cpp:26:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from ./boost/thread/thread_only.hpp:17,
                 from ./boost/thread/thread.hpp:12,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MGF.cpp:29:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from ./boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from ./boost/smart_ptr/detail/yield_k.hpp:23,
                 from ./boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from ./boost/smart_ptr/detail/spinlock.hpp:42,
                 from ./boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from ./boost/smart_ptr/shared_ptr.hpp:29,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/data/common/ParamTypes.hpp:33,
                 from ./pwiz/data/msdata/MSData.hpp:30:
./boost/config/pragma_message.hpp:24:34: 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.’
   24 | # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
      |                                  ^~~~~~~
./boost/bind.hpp:36:1: note: in expansion of macro ‘BOOST_PRAGMA_MESSAGE’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from ./boost/thread/thread_only.hpp:17,
                 from ./boost/thread/thread.hpp:12,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:32:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from ./boost/thread/thread_only.hpp:17,
                 from ./boost/thread/thread.hpp:12,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_MSn.cpp:31:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o
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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from ./pwiz/utility/misc/Std.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:26:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_mz5.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:28:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
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:
./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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/thread/thread_only.hpp:17,
                 from ./boost/thread/thread.hpp:12,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mz5.cpp:29:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp: In member function ‘void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)’:
pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: ‘byteCount’ may be used uninitialized [-Wmaybe-uninitialized]
  302 |         filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: ‘byteCount’ was declared here
  131 |     size_t byteCount;
      |            ^~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: ‘byteBuffer’ may be used uninitialized [-Wmaybe-uninitialized]
  302 |         filterArray<zlib_compressor>(byteBuffer, byteCount,compressed);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: ‘byteBuffer’ was declared here
  132 |     const void* byteBuffer;
      |                 ^~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from ./boost/thread/thread_only.hpp:17,
                 from ./boost/thread/thread.hpp:12,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_mzXML.cpp:30:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
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=]
   84 |     } catch (index_not_found e){
      |                              ^
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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]
 1657 |     if (usedConfig.byteOrder == BinaryDataEncoder::ByteOrder_BigEndian)
      |     ^~
pwiz/data/msdata/IO.cpp:1660:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 1660 |         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 std::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]
 2132 |             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 std::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]
 2836 |         else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ ||
      |                  ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from ./boost/thread/thread_only.hpp:17,
                 from ./boost/thread/thread.hpp:12,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumList_BTDX.cpp:30:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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]
  125 |     return (done() && &that.spectrumList_==&pastEndMarker_ ||
      |             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/msdata/SpectrumIterator.cpp:127:49: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  127 |             &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]
  141 |     return !scanNumbers_.empty() && currentScanNumber_==scanNumbers_.end() ||
      |            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from pwiz/data/msdata/Reader.hpp:29,
                 from pwiz/data/msdata/MSDataFile.hpp:30:
./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]
   40 |                mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from pwiz/data/msdata/SpectrumList_MSn.hpp:29,
                 from pwiz/data/msdata/Serializer_MSn.hpp:29,
                 from pwiz/data/msdata/MSDataFile.cpp:31:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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]
  114 |     } else if (init == mask) {
      |                ~~~~~^~~~~~~
In file included from /usr/include/c++/13/iostream:41,
                 from pwiz/data/msdata/MSNumpress.cpp:27:
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)’ at pwiz/data/msdata/MSNumpress.cpp:403:33:
/usr/include/c++/13/ostream:204:25: warning: ‘extrapol’ may be used uninitialized [-Wmaybe-uninitialized]
  204 |       { return _M_insert(__n); }
      |                ~~~~~~~~~^~~~~
pwiz/data/msdata/MSNumpress.cpp: In function ‘size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)’:
pwiz/data/msdata/MSNumpress.cpp:346:15: note: ‘extrapol’ was declared here
  346 |     long long extrapol;
      |               ^~~~~~~~
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)’ at pwiz/data/msdata/MSNumpress.cpp:404:26:
/usr/include/c++/13/ostream:204:25: warning: ‘y’ may be used uninitialized [-Wmaybe-uninitialized]
  204 |       { return _M_insert(__n); }
      |                ~~~~~~~~~^~~~~
pwiz/data/msdata/MSNumpress.cpp: In function ‘size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)’:
pwiz/data/msdata/MSNumpress.cpp:347:15: note: ‘y’ was declared here
  347 |     long long y;
      |               ^
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from ./boost/multi_index/detail/hash_index_args.hpp:17,
                 from ./boost/multi_index/hashed_index_fwd.hpp:16,
                 from ./boost/multi_index/hashed_index.hpp:43,
                 from ./pwiz/utility/misc/mru_list.hpp:26,
                 from pwiz/data/msdata/MemoryMRUCache.hpp:27,
                 from pwiz/data/msdata/SpectrumListCache.hpp:28:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from ./pwiz/utility/misc/BinaryData.hpp:30:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from ./pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
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:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from ./pwiz/utility/misc/Std.hpp:28,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:24:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from ./boost/functional/hash.hpp:6,
                 from ./pwiz/data/msdata/SpectrumListBase.hpp:30,
                 from ./pwiz/data/msdata/SpectrumListWrapper.hpp:28,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:27:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from ./boost/thread/thread_only.hpp:17,
                 from ./boost/thread/thread.hpp:12,
                 from ./boost/thread.hpp:13,
                 from pwiz/data/msdata/SpectrumWorkerThreads.cpp:31:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 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:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
In file included from pwiz/data/identdata/IdentDataFile.cpp:26:
pwiz/data/identdata/TextWriter.hpp: In member function ‘pwiz::identdata::TextWriter& pwiz::identdata::TextWriter::operator()(const pwiz::identdata::IdentData&)’:
pwiz/data/identdata/TextWriter.hpp:887:46: warning: ignoring return value of ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator> std::operator+(const _CharT*, const __cxx11::basic_string<_CharT, _Traits, _Allocator>&) [with _CharT = char; _Traits = char_traits<char>; _Alloc = allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
  887 |                ("version: " + mzid.version());
      |                                              ^
In file included from /usr/include/c++/13/string:54,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from pwiz/data/identdata/IdentData.hpp:29:
/usr/include/c++/13/bits/basic_string.h:3571:5: note: declared here
 3571 |     operator+(const _CharT* __lhs,
      |     ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
In file included from ./boost_aux/boost/enum.hpp:21,
                 from ./pwiz/data/common/Unimod.hpp:31,
                 from pwiz/data/identdata/IdentData.cpp:30:
./pwiz/data/common/Unimod.hpp: In function ‘bool pwiz::data::unimod::operator==(const Site::domain&, const Site&)’:
./boost_aux/boost/enum/macros.hpp:226:85: warning: in C++20 this comparison calls the current function recursively with reversed arguments
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                                                                                 ~~~~^~~~~~
./boost_aux/boost/enum/macros.hpp:234:5: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
  234 |     BOOST_ENUM_DOMAIN_OPERATORS(_name) \
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/data/common/Unimod.hpp:69:1: note: in expansion of macro ‘BOOST_BITFIELD_DOMAIN_OPERATORS’
   69 | BOOST_BITFIELD_DOMAIN_OPERATORS(Site)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/data/common/Unimod.hpp: In function ‘bool pwiz::data::unimod::operator==(const Position::domain&, const Position&)’:
./boost_aux/boost/enum/macros.hpp:226:85: warning: in C++20 this comparison calls the current function recursively with reversed arguments
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                                                                                 ~~~~^~~~~~
./pwiz/data/common/Unimod.hpp:78:1: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
   78 | BOOST_ENUM_DOMAIN_OPERATORS(Position)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/data/common/Unimod.hpp: In function ‘bool pwiz::data::unimod::operator==(const Classification::domain&, const Classification&)’:
./boost_aux/boost/enum/macros.hpp:226:85: warning: in C++20 this comparison calls the current function recursively with reversed arguments
  226 |     inline bool operator== (const _name::domain& lhs, const _name& rhs) {return rhs == lhs;} \
      |                                                                                 ~~~~^~~~~~
./boost_aux/boost/enum/macros.hpp:234:5: note: in expansion of macro ‘BOOST_ENUM_DOMAIN_OPERATORS’
  234 |     BOOST_ENUM_DOMAIN_OPERATORS(_name) \
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./pwiz/data/common/Unimod.hpp:97:1: note: in expansion of macro ‘BOOST_BITFIELD_DOMAIN_OPERATORS’
   97 | BOOST_BITFIELD_DOMAIN_OPERATORS(Classification)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 from ./pwiz/utility/chemistry/Ion.hpp:28,
                 from pwiz/data/identdata/IdentData.cpp:28:
./pwiz/utility/misc/virtual_map.hpp: At global scope:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32,
                 from pwiz/data/identdata/IdentData.hpp:30,
                 from pwiz/data/identdata/IdentData.cpp:31:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 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/DefaultReaderList.hpp:29,
                 from pwiz/data/identdata/DefaultReaderList.cpp:29:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 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:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 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:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
In file included from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/identdata/Serializer_protXML.cpp:36:
./pwiz/utility/misc/BinaryData.hpp:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from pwiz/data/identdata/IdentData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
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]
  478 |     bool strict;
      |          ^~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning:   ‘int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides’ [-Wreorder]
   85 |     int nPeptides;
      |         ^~~~~~~~~
pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning:   when initialized here [-Wreorder]
   91 |     Handler_protXML(IdentData& mzid,
      |     ^~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 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:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
In file included from ./pwiz/data/msdata/MSData.hpp:29,
                 from pwiz/data/identdata/Serializer_pepXML.cpp:33:
./pwiz/utility/misc/BinaryData.hpp:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_construct.h:61,
                 from /usr/include/c++/13/bits/char_traits.h:57,
                 from /usr/include/c++/13/string:42,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from pwiz/data/identdata/IdentData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
pwiz/data/identdata/Serializer_pepXML.cpp: In function ‘void pwiz::identdata::{anonymous}::write_spectrum_queries(pwiz::minimxml::XMLWriter&, const pwiz::identdata::IdentData&, const std::string&, const pwiz::util::IterationListenerRegistry*)’:
pwiz/data/identdata/Serializer_pepXML.cpp:801:52: warning: ‘lastSpectrumIndex’ may be used uninitialized [-Wmaybe-uninitialized]
  801 |             if (sii.chargeState != lastChargeState || spectrumIndex != lastSpectrumIndex)
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/data/identdata/Serializer_pepXML.cpp:775:26: note: ‘lastSpectrumIndex’ was declared here
  775 |     int lastChargeState, lastSpectrumIndex;
      |                          ^~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 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:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 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:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
In file included from pwiz/data/identdata/IO.cpp:28:
pwiz/data/identdata/TextWriter.hpp: In member function ‘pwiz::identdata::TextWriter& pwiz::identdata::TextWriter::operator()(const pwiz::identdata::IdentData&)’:
pwiz/data/identdata/TextWriter.hpp:887:46: warning: ignoring return value of ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator> std::operator+(const _CharT*, const __cxx11::basic_string<_CharT, _Traits, _Allocator>&) [with _CharT = char; _Traits = char_traits<char>; _Alloc = allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
  887 |                ("version: " + mzid.version());
      |                                              ^
In file included from /usr/include/c++/13/string:54,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from pwiz/data/identdata/IdentData.hpp:29:
/usr/include/c++/13/bits/basic_string.h:3571:5: note: declared here
 3571 |     operator+(const _CharT* __lhs,
      |     ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 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:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
In file included from pwiz/data/identdata/References.cpp:26:
pwiz/data/identdata/TextWriter.hpp: In member function ‘pwiz::identdata::TextWriter& pwiz::identdata::TextWriter::operator()(const pwiz::identdata::IdentData&)’:
pwiz/data/identdata/TextWriter.hpp:887:46: warning: ignoring return value of ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator> std::operator+(const _CharT*, const __cxx11::basic_string<_CharT, _Traits, _Allocator>&) [with _CharT = char; _Traits = char_traits<char>; _Alloc = allocator<char>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
  887 |                ("version: " + mzid.version());
      |                                              ^
In file included from /usr/include/c++/13/string:54,
                 from /usr/include/c++/13/stdexcept:39,
                 from ./pwiz/utility/misc/Exception.hpp:28,
                 from pwiz/data/identdata/IdentData.hpp:29:
/usr/include/c++/13/bits/basic_string.h:3571:5: note: declared here
 3571 |     operator+(const _CharT* __lhs,
      |     ^~~~~~~~
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]
  148 |         else if (dynamic_cast<Person*>(c.get()))
      |                 ^
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
In file included from ./pwiz/utility/chemistry/Chemistry.hpp:32,
                 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/MascotReader.hpp:28,
                 from pwiz/data/identdata/MascotReader.cpp:26:
./pwiz/utility/misc/virtual_map.hpp:218:18: warning: ‘void pwiz::util::virtual_map<keyT, valueT, _Pr, _Alloc>::swap(pwiz::util::virtual_map<keyT, valueT, typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare, typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type>&) [with keyT = int; valueT = pwiz::proteome::ModificationList; _Pr = std::less<int>; _Alloc = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >; typename std::map<_Key, _Tp, _Compare, _Allocator>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Allocator>::allocator_type = std::allocator<std::pair<const int, pwiz::proteome::ModificationList> >]’ was hidden [-Woverloaded-virtual=]
  218 |     virtual void swap(virtual_map<keyT, valueT, key_compare, allocator_type>& x)
      |                  ^~~~
In file included from ./pwiz/data/proteome/Peptide.hpp:183,
                 from ./pwiz/data/proteome/Digestion.hpp:32:
./pwiz/data/proteome/Modification.hpp:189:18: note:   by ‘virtual void pwiz::proteome::ModificationMap::swap(pwiz::proteome::ModificationMap&)’
  189 |     virtual void swap(ModificationMap&);
      |                  ^~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/proteome/Modification.cpp -o pwiz/data/proteome/Modification.o
pwiz/data/proteome/Modification.cpp:89:5: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   89 |     auto_ptr<Formula> formula_;
      |     ^~~~~~~~
In file included from /usr/include/c++/13/memory:78,
                 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:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
pwiz/utility/minimxml/SAXParser.cpp: In function ‘void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)’:
pwiz/utility/minimxml/SAXParser.cpp:543:61: warning: offset ‘1’ outside bounds of constant string [-Warray-bounds=]
  543 |                 Handler::Status status = wrangler.endElement(buffer.c_str()+1, position);
      |                                          ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: ‘inCDATA’ may be used uninitialized [-Wmaybe-uninitialized]
  549 |                 if (inCDATA)
      |                 ^~
pwiz/utility/minimxml/SAXParser.cpp:501:14: note: ‘inCDATA’ was declared here
  501 |         bool inCDATA;
      |              ^~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
pwiz/utility/misc/IntegerSet.cpp: In member function ‘bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const’:
pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  307 |     return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ ||
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o
pwiz/utility/misc/BinaryData.cpp:303: warning: ignoring ‘#pragma managed ’ [-Wunknown-pragmas]
  303 | #pragma managed(push, off)
      | 
pwiz/utility/misc/BinaryData.cpp:475: warning: ignoring ‘#pragma managed ’ [-Wunknown-pragmas]
  475 | #pragma managed(pop)
      | 
In file included from pwiz/utility/misc/BinaryData.cpp:24:
pwiz/utility/misc/BinaryData.hpp:54:54: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   54 |     class PWIZ_API_DECL const_iterator : public std::iterator<std::random_access_iterator_tag, const T>
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:65,
                 from /usr/include/c++/13/algorithm:60,
                 from pwiz/utility/misc/BinaryData.hpp:29:
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   88 |     class PWIZ_API_DECL iterator : public std::iterator<std::random_access_iterator_tag, T>
      |                                                ^~~~~~~~
/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/thread/thread_only.hpp:17,
                 from ./boost/thread/thread.hpp:12,
                 from ./boost/thread.hpp:13,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:77:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
In file included from ./boost/functional/hash.hpp:6,
                 from ./boost/thread/detail/thread.hpp:41,
                 from ./boost/thread/thread_only.hpp:22:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/locale:41,
                 from ./boost/iostreams/detail/config/codecvt.hpp:63,
                 from ./boost/iostreams/positioning.hpp:21,
                 from pwiz/utility/misc/random_access_compressed_ifstream.hpp:71,
                 from pwiz/utility/misc/random_access_compressed_ifstream.cpp:67:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
g++ -std=gnu++20 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
In file included from ./boost/thread/thread_only.hpp:17,
                 from boost/libs/thread/src/pthread/thread.cpp:11:
./boost/thread/pthread/thread_data.hpp: In member function ‘void boost::thread_attributes::set_stack_size(std::size_t)’:
./boost/thread/pthread/thread_data.hpp:61:19: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare]
   61 |           if (size<PTHREAD_STACK_MIN) size=PTHREAD_STACK_MIN;
      |                   ^
In file included from ./boost/functional/hash.hpp:6,
                 from ./boost/thread/detail/thread.hpp:41,
                 from ./boost/thread/thread_only.hpp:22:
./boost/container_hash/hash.hpp: At global scope:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  131 |         struct hash_base : std::unary_function<T, std::size_t> {};
      |                                 ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from ./boost/thread/exceptions.hpp:20,
                 from ./boost/thread/pthread/thread_data.hpp:10:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ -std=gnu++20 -shared -L/usr/local/lib -o mzR.so 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/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o -lpthread /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5.a -L/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rhdf5lib/lib -lsz -lm -ldl -lcurl -lssl -lcrypto
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-mzR/00new/mzR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mzR)

Tests output

mzR.Rcheck/tests/runTests.Rout


R Under development (unstable) (2026-03-06 r89561) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

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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")

 IMPORTANT: msdata will be deprecated and replaced by the new
 MsDataHub package -- see https://bioconductor.org/packages/MsDataHub.
 Please open an issue at https://github.com/rformassspectrometry/MsDataHub/issues
 to inform us of any data from msdata that would need to be moved to MsDataHub.

> 
> 
> ## Catch warnings as well:
> #options(warn = 2)
> 
> BiocGenerics:::testPackage("mzR")
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 
Unknown IO errorfailed to load external entity "http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_3.2.xsd"
Element '{http://www.w3.org/2001/XMLSchema}include': Failed to load the document 'http://sashimi.sourceforge.net/schema_revision/mzXML_3.2/mzXML_3.2.xsd' for inclusion.


RUNIT TEST PROTOCOL -- Thu Mar 12 15:05:51 2026 
*********************************************** 
Number of test functions: 30 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mzR RUnit Tests - 30 test functions, 0 errors, 0 failures
Number of test functions: 30 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: pwiz not yet initialized. 
2: pwiz not yet initialized. 
3: In XML::xmlTreeParse(system.file("extdata", "mzXML_idx_3.2.xsd.xml",  :
  NULL value for external reference
> 
> proc.time()
   user  system elapsed 
 22.306   0.871  23.110

Example timings

mzR.Rcheck/mzR-Ex.timings

name	user	system	elapsed
copyWriteMSData	0.070	0.010	0.086
isolationWindow-methods	0.721	0.123	0.844
metadata	0.115	0.019	0.164
mzR-class	0.024	0.002	0.035
openMSfile	0.041	0.002	0.042
peaks	0.610	0.038	0.651
writeMSData	0.046	0.005	0.049