Steffen Neumann
| Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/mzR |
| git_branch: devel |
| git_last_commit: 0368dbf |
| git_last_commit_date: 2024-11-19 11:40:48 -0500 (Tue, 19 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-04 11:40 -0500 (Tue, 04 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4716 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4478 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4489 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4442 |
| 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 1393/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mzR 2.41.1 (landing page) Steffen Neumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 2.41.1 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mzR_2.41.1.tar.gz |
| StartedAt: 2025-02-04 00:49:11 -0500 (Tue, 04 Feb 2025) |
| EndedAt: 2025-02-04 00:50:36 -0500 (Tue, 04 Feb 2025) |
| EllapsedTime: 85.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: mzR.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:mzR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings mzR_2.41.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mzR.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* 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 ‘2.41.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... 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/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-3.21-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 ... INFO
installed size is 61.7Mb
sub-directories of 1Mb or more:
libs 61.2Mb
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
mzR-class.Rd: Versioned-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.21-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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-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-3.21-bioc/R/bin/R CMD INSTALL mzR
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘mzR’ ...
** this is package ‘mzR’ version ‘2.41.1’
** 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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppPwiz.cpp -o RcppPwiz.o
RcppPwiz.cpp: In member function ‘Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector)’:
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: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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppPwizModule.cpp -o RcppPwizModule.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppIdent.cpp -o RcppIdent.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppIdentModule.cpp -o RcppIdentModule.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
In file included from ./boost/functional/hash.hpp:6,
from ./boost/thread/detail/thread.hpp:41,
from ./boost/thread/thread_only.hpp:22,
from ./boost/thread/thread.hpp:12,
from pwiz/data/common/BinaryIndexStream.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 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
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
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: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,
from pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp:24:
/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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.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/DefaultReaderList.cpp:30:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
131 | struct hash_base : std::unary_function<T, std::size_t> {};
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_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/Serializer_mz5.cpp:29:
./boost/container_hash/hash.hpp:131:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
131 | struct hash_base : std::unary_function<T, std::size_t> {};
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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(
| ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/MSData.cpp -o pwiz/data/msdata/MSData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.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/MSDataFile.cpp:31:
./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,
from pwiz/data/msdata/MSDataFile.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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
In file included from ./boost/functional/hash.hpp:6,
from ./boost/thread/detail/thread.hpp:41,
from ./boost/thread/thread_only.hpp:22,
from ./boost/thread/thread.hpp:12,
from ./boost/thread.hpp:13,
from pwiz/utility/misc/random_access_compressed_ifstream.cpp:77:
./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-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -DR_NO_REMAP -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
In file included from ./boost/functional/hash.hpp:6,
from ./boost/thread/detail/thread.hpp:41,
from ./boost/thread/thread_only.hpp:22,
from boost/libs/thread/src/pthread/thread.cpp:11:
./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,
from ./boost/thread/thread_only.hpp:17:
/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-3.21-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-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.21-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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
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Platform: x86_64-pc-linux-gnu
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Type 'license()' or 'licence()' for distribution details.
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> 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 -- Tue Feb 4 00:50:27 2025
***********************************************
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
30.205 0.924 31.523
mzR.Rcheck/mzR-Ex.timings
| name | user | system | elapsed | |
| copyWriteMSData | 0.091 | 0.012 | 0.103 | |
| isolationWindow-methods | 1.016 | 0.136 | 1.150 | |
| metadata | 0.169 | 0.024 | 0.195 | |
| mzR-class | 0.036 | 0.003 | 0.040 | |
| openMSfile | 0.061 | 0.000 | 0.060 | |
| peaks | 0.872 | 0.046 | 0.916 | |
| writeMSData | 0.062 | 0.002 | 0.064 | |