Internal Compiler Error When Installing mzR

[Doctorluka]

Hi,
I am experiencing an internal compiler error when trying to install the mzR package on my system (ubuntu 22.04 in WSL, R 4.3.2). The issue occurs regardless of whether I use GCC versions 9, 10 or 11.

Here, I show the error when installing mzR using BiocManager in gcc 11 version.

> BiocManager::install("mzR")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for
details.
Replacement repositories:
    CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/
Bioconductor version 3.18 (BiocManager 1.30.25), R 4.3.2 (2023-10-31)
Installing package(s) 'mzR'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/mzR_2.36.0.tar.gz'
Content type 'application/gzip' length 7673297 bytes (7.3 MB)
==================================================
downloaded 7.3 MB

* installing *source* package ‘mzR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
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"/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'/home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -I'/home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include' -I/usr/local/include   -O0 -fpic  -g -O2  -c RcppPwiz.cpp -o RcppPwiz.o
g++ -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'/home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -I'/home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include' -I/usr/local/include   -O0 -fpic  -g -O2  -c RcppPwizModule.cpp -o RcppPwizModule.o
during GIMPLE pass: ch
In file included from /home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp/Module.h:523,
                 from /home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp.h:69,
                 from RcppPwizModule.cpp:1:
/home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp/module/class.h: In member function ‘bool Rcpp::class_<Class>::has_default_constructor() [with Class = RcppPwiz]’:
/home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include/Rcpp/module/class.h:163:14: internal compiler error: Segmentation fault
  163 |         bool has_default_constructor(){
      |              ^~~~~~~~~~~~~~~~~~~~~~~
0xe34ddb internal_error(char const*, ...)
	???:0
0xf1f9e9 diagnostic_set_info(diagnostic_info*, char const*, __va_list_tag (*) [1], rich_location*, diagnostic_t)
	???:0
0xe34ddb internal_error(char const*, ...)
	???:0
0xe2b903 fancy_abort(char const*, int, char const*)
	???:0
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See <file:///usr/share/doc/gcc-11/README.Bugs> for instructions.
make: *** [/opt/R/4.3.2/lib/R/etc/Makeconf:200: RcppPwizModule.o] Error 1
ERROR: compilation failed for package ‘mzR’
* removing ‘/home/joe/R/x86_64-pc-linux-gnu-library/4.3/mzR’

The downloaded source packages are in
	‘/tmp/Rtmp0xnU8U/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /opt/R/4.3.2/lib/R/library
  packages:
    boot, cluster, codetools, foreign, KernSmooth, lattice, mgcv, nlme, rpart, survival
Old packages: 'anticlust', 'aplot', 'arrow', 'bbotk', 'broom', 'car', 'ccaPP', 'CelliD', 'crul', 'datawizard', 'dbscan',
  'densvis', 'distributional', 'downlit', 'e1071', 'emmeans', 'flextable', 'fpc', 'gdtools', 'geomtextpath', 'gert', 'ggfun',
  'ggiraph', 'glue', 'graphlayouts', 'hardhat', 'harmony', 'hdf5r', 'Hmisc', 'htmlTable', 'httr2', 'insight', 'ipred',
  'leidenbase', 'lme4', 'loo', 'magick', 'markdown', 'metatools', 'minqa', 'mlr3', 'mlr3fselect', 'mlr3hyperband',
  'mlr3learners', 'mlr3mbo', 'mlr3measures', 'mlr3misc', 'mlr3pipelines', 'mlr3tuning', 'mlr3tuningspaces', 'mlr3verse',
  'mlr3viz', 'multcomp', 'NMF', 'officer', 'openxlsx', 'ordinal', 'pals', 'paradox', 'pbkrtest', 'pcaPP', 'pkgdown',
  'pkgload', 'polspline', 'posterior', 'prodlim', 'profvis', 'psych', 'qlcMatrix', 'qs', 'quantreg', 'QuickJSR',
  'RApiSerialize', 'RcppRoll', 'recipes', 'reprex', 'rjson', 'robustbase', 'roxygen2', 'RSQLite', 'rvg', 's2', 'scatterpie',
  'Seurat', 'sf', 'Signac', 'sjmisc', 'spData', 'spdep', 'StanHeaders', 'terra', 'tm', 'TraMineR', 'usethis', 'uwot',
  'waldo', 'WeightedCluster', 'WGCNA', 'yulab.utils'
Update all/some/none? [a/s/n]: 
n

gcc version:

gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

If you need any further information, please let me know at your earliest convenience. Thank you!

[Doctorluka]

my sessionInfo():

R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8   
 [6] LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           LC_TELEPHONE=C        
[11] LC_MEASUREMENT=C.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_1.30.25 compiler_4.3.2      tools_4.3.2  

[sneumann]

Hi,
hm, haven't seen those in a while :-( So there are some systems where this works:
https://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/
so it might be specific to your setup. If I compare to my setup, an immediate difference might be that your R is compiled against /usr/lib/x86_64-linux-gnu/openblas-pthread/ (from [libopenblas0-pthread](https://packages.ubuntu.com/jammy/libopenblas0-pthread)), while here I have /usr/lib/x86_64-linux-gnu/blas/ (from libblas3:amd64).

In the old days, I encountered internal compiler errors with too much optimisation: Do you get the same error if you copy&paste the compile command manually without -O0 -O2 (see below) ?

And/or, could you try to swap the BLAS libraries, so we can confirm they are the factor causing the SEGV ? Bonus points if you create a Dockerfile to reproduce, so others might be able to chime in, possibly even the gcc or openblas folks.

Yours,
Steffen

g++ -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'/home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rcpp/include' -I'/home/joe/R/x86_64-pc-linux-gnu-library/4.3/Rhdf5lib/include' -I/usr/local/include -fpic  -g -c RcppPwizModule.cpp -o RcppPwizModule.o