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Error: package or namespace load failed for ‘mzR’ in dyn.load(file, DLLpath = DLLpath, ...) (centos7/R 4.3.2) #287

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wangshisheng opened this issue Nov 14, 2023 · 5 comments
Open

Error: package or namespace load failed for ‘mzR’ in dyn.load(file, DLLpath = DLLpath, ...) (centos7/R 4.3.2) #287

wangshisheng opened this issue Nov 14, 2023 · 5 comments

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@wangshisheng
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Dear sneumann,

When I installed the mzR package using "BiocManager::install("mzR")" in centos7/R 4.3.2, it gived me the error below:
...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘mzR’
finding HTML links ... done
copyWriteMSData html
isolationWindow-methods html
metadata html
mzR-class html
finding level-2 HTML links ... done

openMSfile                              html  
peaks                                   html  
pwiz-version                            html  
writeMSData                             html

** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘mzR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs/mzR.so':
/opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs/mzR.so: undefined symbol: _ZNK2H510H5Location13createDataSetERKSsRKNS_8DataTypeERKNS_9DataSpaceERKNS_17DSetCreatPropListERKNS_15DSetAccPropListERKNS_17LinkCreatPropListE
Error: loading failed
Execution halted
ERROR: loading failed

  • removing ‘/opt/R/4.3.2/lib/R/library/mzR’

Below is my sessioninfo:

sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so; LAPACK version 3.8.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Asia/Shanghai
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.3.2 tools_4.3.2

Could you give some helps about this? Thanks a lot!

Shisheng
@sneumann
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Hi, I don't think I have seen that specific error message so far.
The unable to load shared object indicates that a symbol for required shared *.so library can't be found, which typically happens if there are several versions and there is an inconsistency between the version from which the *.h header files and later the used *.so library occurs.
Using the c++filt tool I can demangle the cryptic symbol name:

echo '_ZNK2H510H5Location13createDataSetERKSsRKNS_8DataTypeERKNS_9DataSpaceERKNS_17DSetCreatPropListERKNS_15DSetAccPropListERKNS_17LinkCreatPropListE' | c++filt

H5::H5Location::createDataSet(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, H5::DataType const&, H5::DataSpace const&, H5::DSetCreatPropList const&, H5::DSetAccPropList const&, H5::LinkCreatPropList const&) const

So, my guess is that there are several versions of libhdf5 installations on that computer. Can you find more than one instance of libnetcdf.so e.g. in /usr/lib/.../libnetcdf.so and another one in /opt or your $HOME ?!

Can you provide the output of ldd /opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs/mzR.so ?
Look out for libnetcdf.so in the output.

Thanks,
Steffen

@wangshisheng
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wangshisheng commented Nov 15, 2023 •
edited
Loading

Hi Steffen,

You are right. I tried again and found that when installing mzR, there was no mzR.so file in the temp folder (/opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs), actually this temp folder was empty.

Here are the libnetcdf.so files:

[wss@localhost ~]# sudo locate libnetcdf
/usr/lib64/libnetcdf.settings
/usr/lib64/libnetcdf.so
/usr/lib64/libnetcdf.so.7
/usr/lib64/libnetcdf.so.7.2.0

Perhaps there are several versions of libnetcdf.so here?

Then I check the libhdf5:

[wss@localhost ~]# sudo yum list installed | grep hdf5
hdf5.x86_64 1.8.12-13.el7 @epel
hdf5-devel.x86_64 1.8.12-13.el7 @epel

Thanks a lot,
Shisheng

@sneumann
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Hi, so the multiple libnetcdf.so* above are no problem, many of them are symbolic links linking to the same file. Also, the yum output shows both packages are the same version. Plus, after checking now, they are actually not even used in mzR (anymore), sorry for misleading you.

Can you show in the long output during R CMD INSTALL mzR, what I need is any one of the many lines starting with gnu++11 -I ... and the last very long line starting with g++ -std=gnu++11 -shared ...:

g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
[...]
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o mzR.so RcppPwiz.o RcppPwizModule.o RcppIdent.o RcppIdentModule.o ./boost/libs/system/src/error_code.o [...] ./boost/libs/thread/src/pthread/once.o ./boost/libs/thread/src/pthread/thread.o -lpthread /usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/usr/lib/R/lib -lR

What I need to see is if -I'/usr/local/lib/R/site-library/Rhdf5lib/include and /usr/local/lib/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a are both used. If the wrong include files are used, that will also cause confusion for the linker.
Yours, Steffen

@wangshisheng
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Hi Steffen,

Yes, here are them:

> BiocManager::install("mzR")
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 (2023-10-31)
Installing package(s) 'mzR'
trying URL 'https://mirrors.nju.edu.cn/bioconductor/packages/3.18/bioc/src/contrib/mzR_2.36.0.tar.gz'
Content type 'application/octet-stream' length 7673297 bytes (7.3 MB)
==================================================
downloaded 7.3 MB

* installing *source* package ‘mzR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 7.2.0’
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
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c RcppPwiz.cpp -o RcppPwiz.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c RcppPwizModule.cpp -o RcppPwizModule.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c RcppIdent.cpp -o RcppIdent.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c RcppIdentModule.cpp -o RcppIdentModule.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/regex/src/posix_api.cpp -o boost/libs/regex/src/posix_api.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/regex/src/regex_debug.cpp -o boost/libs/regex/src/regex_debug.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/regex/src/regex.cpp -o boost/libs/regex/src/regex.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/regex/src/wide_posix_api.cpp -o boost/libs/regex/src/wide_posix_api.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/regex/src/static_mutex.cpp -o boost/libs/regex/src/static_mutex.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/iostreams/src/zlib.cpp -o boost/libs/iostreams/src/zlib.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/iostreams/src/file_descriptor.cpp -o boost/libs/iostreams/src/file_descriptor.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/chrono/src/chrono.cpp -o boost/libs/chrono/src/chrono.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/chrono/src/process_cpu_clocks.cpp -o boost/libs/chrono/src/process_cpu_clocks.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/chrono/src/thread_clock.cpp -o boost/libs/chrono/src/thread_clock.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/Version.cpp -o pwiz/data/msdata/Version.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/Version.cpp -o pwiz/data/identdata/Version.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/common/MemoryIndex.cpp -o pwiz/data/common/MemoryIndex.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/common/CVTranslator.cpp -o pwiz/data/common/CVTranslator.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/common/cv.cpp -o pwiz/data/common/cv.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/common/ParamTypes.cpp -o pwiz/data/common/ParamTypes.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/common/BinaryIndexStream.cpp -o pwiz/data/common/BinaryIndexStream.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/common/diff_std.cpp -o pwiz/data/common/diff_std.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/common/Unimod.cpp -o pwiz/data/common/Unimod.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/mz5/Configuration_mz5.cpp -o pwiz/data/msdata/mz5/Configuration_mz5.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/mz5/Connection_mz5.cpp -o pwiz/data/msdata/mz5/Connection_mz5.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/mz5/Datastructures_mz5.cpp -o pwiz/data/msdata/mz5/Datastructures_mz5.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/mz5/ReferenceRead_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceRead_mz5.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/mz5/ReferenceWrite_mz5.cpp -o pwiz/data/msdata/mz5/ReferenceWrite_mz5.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/mz5/Translator_mz5.cpp -o pwiz/data/msdata/mz5/Translator_mz5.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/DefaultReaderList.cpp -o pwiz/data/msdata/DefaultReaderList.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/ChromatogramList_mzML.cpp -o pwiz/data/msdata/ChromatogramList_mzML.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/ChromatogramList_mz5.cpp -o pwiz/data/msdata/ChromatogramList_mz5.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/examples.cpp -o pwiz/data/msdata/examples.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/Serializer_mzML.cpp -o pwiz/data/msdata/Serializer_mzML.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/Serializer_MSn.cpp -o pwiz/data/msdata/Serializer_MSn.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/Reader.cpp -o pwiz/data/msdata/Reader.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/Serializer_mz5.cpp -o pwiz/data/msdata/Serializer_mz5.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/Serializer_MGF.cpp -o pwiz/data/msdata/Serializer_MGF.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/Serializer_mzXML.cpp -o pwiz/data/msdata/Serializer_mzXML.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumListBase.cpp -o pwiz/data/msdata/SpectrumListBase.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumList_MGF.cpp -o pwiz/data/msdata/SpectrumList_MGF.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumList_mzML.cpp -o pwiz/data/msdata/SpectrumList_mzML.o
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,
                 from pwiz/data/msdata/SpectrumListBase.hpp:28,
                 from pwiz/data/msdata/SpectrumList_mzML.hpp:29,
                 from pwiz/data/msdata/SpectrumList_mzML.cpp:26:
./boost/config/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(
      | ^~~~~~~~~~~~~~~~~~~~
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumList_MSn.cpp -o pwiz/data/msdata/SpectrumList_MSn.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumList_mz5.cpp -o pwiz/data/msdata/SpectrumList_mz5.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/BinaryDataEncoder.cpp -o pwiz/data/msdata/BinaryDataEncoder.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/Diff.cpp -o pwiz/data/msdata/Diff.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -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 string&, char) const’:
pwiz/data/msdata/MSData.cpp:1086:20: warning: control reaches end of non-void function [-Wreturn-type]
 1086 |     vector<string> abbreviatedTokens, actualTokens;
      |                    ^~~~~~~~~~~~~~~~~
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/References.cpp -o pwiz/data/msdata/References.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumList_mzXML.cpp -o pwiz/data/msdata/SpectrumList_mzXML.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/IO.cpp -o pwiz/data/msdata/IO.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumList_BTDX.cpp -o pwiz/data/msdata/SpectrumList_BTDX.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumInfo.cpp -o pwiz/data/msdata/SpectrumInfo.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/LegacyAdapter.cpp -o pwiz/data/msdata/LegacyAdapter.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumIterator.cpp -o pwiz/data/msdata/SpectrumIterator.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/MSDataFile.cpp -o pwiz/data/msdata/MSDataFile.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/MSNumpress.cpp -o pwiz/data/msdata/MSNumpress.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumListCache.cpp -o pwiz/data/msdata/SpectrumListCache.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/Index_mzML.cpp -o pwiz/data/msdata/Index_mzML.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/msdata/SpectrumWorkerThreads.cpp -o pwiz/data/msdata/SpectrumWorkerThreads.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/IdentDataFile.cpp -o pwiz/data/identdata/IdentDataFile.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/IdentData.cpp -o pwiz/data/identdata/IdentData.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/DefaultReaderList.cpp -o pwiz/data/identdata/DefaultReaderList.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/Reader.cpp -o pwiz/data/identdata/Reader.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/Serializer_protXML.cpp -o pwiz/data/identdata/Serializer_protXML.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/Serializer_pepXML.cpp -o pwiz/data/identdata/Serializer_pepXML.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/Serializer_mzid.cpp -o pwiz/data/identdata/Serializer_mzid.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/IO.cpp -o pwiz/data/identdata/IO.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/References.cpp -o pwiz/data/identdata/References.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/identdata/MascotReader.cpp -o pwiz/data/identdata/MascotReader.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -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 [-Wdeprecated-declarations]
   89 |     auto_ptr<Formula> formula_;
      |     ^~~~~~~~
In file included from /opt/rh/devtoolset-9/root/usr/include/c++/9/memory:80,
                 from ./boost/smart_ptr/detail/sp_counted_impl.hpp:35,
                 from ./boost/smart_ptr/detail/shared_count.hpp:27,
                 from ./boost/smart_ptr/shared_ptr.hpp:17,
                 from ./boost/shared_ptr.hpp:17,
                 from ./pwiz/utility/chemistry/Chemistry.hpp:33,
                 from pwiz/data/proteome/Peptide.hpp:29,
                 from pwiz/data/proteome/Modification.hpp:30,
                 from pwiz/data/proteome/Modification.cpp:27:
/opt/rh/devtoolset-9/root/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/proteome/Digestion.cpp -o pwiz/data/proteome/Digestion.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/proteome/Peptide.cpp -o pwiz/data/proteome/Peptide.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/data/proteome/AminoAcid.cpp -o pwiz/data/proteome/AminoAcid.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/minimxml/XMLWriter.cpp -o pwiz/utility/minimxml/XMLWriter.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/minimxml/SAXParser.cpp -o pwiz/utility/minimxml/SAXParser.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/chemistry/Chemistry.cpp -o pwiz/utility/chemistry/Chemistry.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/chemistry/ChemistryData.cpp -o pwiz/utility/chemistry/ChemistryData.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/chemistry/MZTolerance.cpp -o pwiz/utility/chemistry/MZTolerance.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/IntegerSet.cpp -o pwiz/utility/misc/IntegerSet.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/Base64.cpp -o pwiz/utility/misc/Base64.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/BinaryData.cpp -o pwiz/utility/misc/BinaryData.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/IterationListener.cpp -o pwiz/utility/misc/IterationListener.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/MSIHandler.cpp -o pwiz/utility/misc/MSIHandler.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/Filesystem.cpp -o pwiz/utility/misc/Filesystem.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/TabReader.cpp -o pwiz/utility/misc/TabReader.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/random_access_compressed_ifstream.cpp -o pwiz/utility/misc/random_access_compressed_ifstream.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/SHA1.cpp -o pwiz/utility/misc/SHA1.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/SHA1Calculator.cpp -o pwiz/utility/misc/SHA1Calculator.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/sha1calc.cpp -o pwiz/utility/misc/sha1calc.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c pwiz/utility/misc/String.cpp -o pwiz/utility/misc/String.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/thread/src/pthread/once.cpp -o boost/libs/thread/src/pthread/once.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG    -I'/opt/R/4.3.2/lib/R/library/Rcpp/include' -I'/opt/R/4.3.2/lib/R/library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/thread/src/pthread/thread.cpp -o boost/libs/thread/src/pthread/thread.o
/opt/rh/devtoolset-9/root/usr/bin/g++ -std=c++11 -std=gnu++11 -shared -L/opt/R/4.3.2/lib/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 /opt/R/4.3.2/lib/R/library/Rhdf5lib/lib/libhdf5_cpp.a /opt/R/4.3.2/lib/R/library/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/opt/R/4.3.2/lib/R/lib -lR
installing to /opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘mzR’
    finding HTML links ... done
    copyWriteMSData                         html  
    isolationWindow-methods                 html  
    metadata                                html  
    mzR-class                               html  
    finding level-2 HTML links ... done

    openMSfile                              html  
    peaks                                   html  
    pwiz-version                            html  
    writeMSData                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘mzR’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs/mzR.so':
  /opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs/mzR.so: undefined symbol: _ZNK2H510H5Location13createDataSetERKSsRKNS_8DataTypeERKNS_9DataSpaceERKNS_17DSetCreatPropListERKNS_15DSetAccPropListERKNS_17LinkCreatPropListE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/R/4.3.2/lib/R/library/mzR’

The downloaded source packages are in
	‘/tmp/RtmpDRAtqI/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

Bests,
Shisheng

@wangshisheng
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Hi Steffen,

Please have a check as you need above at your convenience, the issue is still there.
Thanks a lot.

Yours,
Shisheng

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@sneumann @wangshisheng