Steffen Neumann
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/mzR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 942e977 |
| git_last_commit_date: 2024-10-29 09:38:05 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 | ||||
| Package 1388/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mzR 2.40.0 (landing page) Steffen Neumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the mzR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mzR.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. |
| Package: mzR |
| Version: 2.40.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mzR_2.40.0.tar.gz |
| StartedAt: 2024-12-20 03:27:34 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 03:32:35 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 301.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mzR.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings mzR_2.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/mzR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mzR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mzR’ version ‘2.40.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mzR’ can be installed ... WARNING
Found the following significant warnings:
RcppPwiz.cpp:408:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
RcppPwiz.cpp:854:55: 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/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type]
pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type ‘struct pwiz::msdata::SpectrumList_mzXML::index_not_found’ by value [-Wcatch-value=]
pwiz/data/identdata/Serializer_protXML.cpp:478:10: warning: ‘pwiz::identdata::{anonymous}::Handler_protXML::strict’ will be initialized after [-Wreorder]
pwiz/data/identdata/Serializer_protXML.cpp:85:9: warning: ‘int pwiz::identdata::{anonymous}::Handler_protXML::nPeptides’ [-Wreorder]
pwiz/data/identdata/Serializer_protXML.cpp:91:5: warning: when initialized here [-Wreorder]
pwiz/data/proteome/Modification.cpp:89:5: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/mzR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 112.7Mb
sub-directories of 1Mb or more:
libs 112.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/mzR/libs/mzR.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘rand_r’, possibly from ‘rand_r’ (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, 4 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/mzR.Rcheck/00check.log’
for details.
mzR.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL mzR
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘mzR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppPwiz.cpp -o RcppPwiz.o
In file included from pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:30,
from RcppPwiz.h:12,
from RcppPwiz.cpp:1:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp: In member function ‘Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)’:
RcppPwiz.cpp:407:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
407 | if (current_scan < 1 || current_scan > n_scans) {
| ~~~~~~~~~~~~~^~~~~~~~~
RcppPwiz.cpp:408:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
408 | 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:853:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
853 | } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
| ~~~~~~~~~~~^~~~~~~~~~~~~
RcppPwiz.cpp:854:55: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
854 | Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1);
| ~^ ~~~~~~~~~~~~~~~
| | |
| int size_t {aka long unsigned int}
| %ld
RcppPwiz.cpp:863:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::msdata::TimeIntensityPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
863 | 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:1014:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1014 | for (int i = 0; i < scanNumbers.size(); i++)
| ~~^~~~~~~~~~~~~~~~~~~~
RcppPwiz.cpp:1020:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pwiz::msdata::MZIntensityPair>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1020 | for (int k=0; k < pairs.size(); k++)
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppPwizModule.cpp -o RcppPwizModule.o
In file included from pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:30,
from RcppPwiz.h:12,
from RcppPwizModule.cpp:2:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppIdentModule.cpp -o RcppIdentModule.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
In file included from pwiz/data/common/cv.cpp:26876:
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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Configuration_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:31,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
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,
from pwiz/data/msdata/mz5/../../common/cv.hpp:35,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.hpp:27:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
In file included from pwiz/data/msdata/mz5/../Reader.hpp:29,
from pwiz/data/msdata/mz5/../MSDataFile.hpp:30,
from pwiz/data/msdata/mz5/Configuration_mz5.hpp:28,
from pwiz/data/msdata/mz5/Connection_mz5.hpp:28,
from pwiz/data/msdata/mz5/ReferenceWrite_mz5.hpp:32,
from pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp:24:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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 ./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: 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/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_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o
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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
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,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_mzML.hpp:29,
from pwiz/data/msdata/Serializer_mzML.cpp:26:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
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/Serializer_MSn.cpp:25:
./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,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_MSn.hpp:26:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o
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,
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_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
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,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_MGF.hpp:27,
from pwiz/data/msdata/Serializer_MGF.cpp:25:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
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,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/Serializer_mzXML.hpp:29,
from pwiz/data/msdata/Serializer_mzXML.cpp:25:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o
In file included from ./boost/functional/hash.hpp:6,
from pwiz/data/msdata/SpectrumListBase.hpp:30,
from pwiz/data/msdata/SpectrumListBase.cpp:25:
./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,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
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/SpectrumList_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,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28:
/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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
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/SpectrumList_mzML.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,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28:
/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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
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/SpectrumList_MSn.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,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28:
/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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o
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,
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_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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
pwiz/data/msdata/MSData.cpp: In member function ‘virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const’:
pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type]
1115 | }
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
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/SpectrumList_mzXML.cpp:25:
./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,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28:
/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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
In file included from ./boost/functional/hash.hpp:6,
from pwiz/data/msdata/SpectrumListBase.hpp:30,
from pwiz/data/msdata/SpectrumList_BTDX.hpp:30,
from pwiz/data/msdata/SpectrumList_BTDX.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,
from ./pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListBase.hpp:28:
/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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
pwiz/data/msdata/SpectrumIterator.cpp: In member function ‘bool pwiz::msdata::SpectrumIterator::Impl::equal(const pwiz::msdata::SpectrumIterator::Impl&) const’:
pwiz/data/msdata/SpectrumIterator.cpp: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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
In file included from pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:30,
from pwiz/data/msdata/MSDataFile.cpp:26:
./pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function ‘bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const’:
./pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
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,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/MSDataFile.hpp:29:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
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,
from pwiz/data/msdata/SpectrumListCache.cpp:25:
./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,
from pwiz/data/msdata/MSData.hpp:29,
from pwiz/data/msdata/SpectrumListCache.hpp:27:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
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,
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_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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
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: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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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&);
| ^~~~
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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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&);
| ^~~~
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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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&);
| ^~~~
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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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, _Alloc>::key_compare, typename std::map<_Key, _Tp, _Compare, _Alloc>::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, _Alloc>::key_compare = std::less<int>; typename std::map<_Key, _Tp, _Compare, _Alloc>::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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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)
|
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -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++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -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 /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/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)
mzR.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library("mzR")
Loading required package: Rcpp
> library("msdata")
>
>
> ## Catch warnings as well:
> #options(warn = 2)
>
> BiocGenerics:::testPackage("mzR")
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 -- Fri Dec 20 03:32:27 2024
***********************************************
Number of test functions: 29
Number of errors: 0
Number of failures: 0
1 Test Suite :
mzR RUnit Tests - 29 test functions, 0 errors, 0 failures
Number of test functions: 29
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
29.500 0.988 30.606
mzR.Rcheck/mzR-Ex.timings
| name | user | system | elapsed | |
| copyWriteMSData | 0.085 | 0.007 | 0.092 | |
| isolationWindow-methods | 1.017 | 0.084 | 1.097 | |
| metadata | 0.126 | 0.007 | 0.133 | |
| mzR-class | 0.034 | 0.001 | 0.035 | |
| openMSfile | 0.056 | 0.003 | 0.059 | |
| peaks | 0.897 | 0.043 | 0.938 | |
| writeMSData | 0.055 | 0.005 | 0.058 | |