RstudioがmzMLファイルを読み込んだときにクラッシュするR端末がありません

Question

大量仕様のmzMLファイル形式のデータがあります。最新バージョンのR（v3.3.2）と最新のRStudio（v1.1.47）を使用すると、mzMLファイルを読み込むとRStudioのRはクラッシュしますが、Rはターミナルにクラッシュします。

error: mzR.so 0x010c47ab: DW_TAG_member '_M_local_buf' refers to type 0x0110cd75 which extends beyond the bounds of 0x010c47a3 
error: mzR.so 0x00efe9cd: DW_TAG_member '_M_local_buf' refers to type 0x00f369c9 which extends beyond the bounds of 0x00efe9c5 
error: mzR.so 0x000000cc: DW_TAG_member '_M_local_buf' refers to type 0x0000a52f which extends beyond the bounds of 0x000000c4 
* thread #1: tid = 3799, 0x0000000000da88cd rsession`boost::filesystem::path::filename() const + 189, name = 'rsession', stop reason = signal SIGSEGV: invalid address (fault address: 0x83e6de7) 
    * frame #0: 0x0000000000da88cd rsession`boost::filesystem::path::filename() const + 189 
    frame #1: 0x00007f2b01ed4aaf mzR.so`pwiz::msdata::IO::HandlerMSData::startElement(this=0x00007ffcdab7b9f0, name=<unavailable>, attributes=<unavailable>, position=<unavailable>) + 511 at IO.cpp:2666 
    frame #2: 0x00007f2b01fd1593 mzR.so`pwiz::minimxml::SAXParser::(anonymous namespace)::HandlerWrangler::startElement(this=0x00007ffcdab7b5b0, name="mzML", attributes=0x00007ffcdab7b558, position=45) const + 147 at SAXParser.cpp:211 
    frame #3: 0x00007f2b01fd2cfa mzR.so`pwiz::minimxml::SAXParser::parse(is=0x00000000066528c0, handler=0x00007ffcdab7b9f0) + 2810 at SAXParser.cpp:531 
    frame #4: 0x00007f2b01ec1927 mzR.so`pwiz::msdata::IO::read(is=0x00000000066528c0, msd=0x0000000004acc510, spectrumListFlag=IgnoreSpectrumList) + 3671 at IO.cpp:2766 
    frame #5: 0x00007f2b01e5747b mzR.so`pwiz::msdata::Serializer_mzML::Impl::read(this=0x000000000501ff30, is=shared_ptr<std::basic_istream<char, std::char_traits<char> > > @ 0x00007ffcdab7c8e0, msd=0x0000000004acc510) const + 107 at Serializer_mzML.cpp:223 
    frame #6: 0x00007f2b01e57b2a mzR.so`pwiz::msdata::Serializer_mzML::read(this=<unavailable>, is=<unavailable>, msd=<unavailable>) const + 58 at Serializer_mzML.cpp:250 
    frame #7: 0x00007f2b01e43964 mzR.so`pwiz::msdata::Reader_mzML::read(this=<unavailable>, filename="/software/R_libs/R332_bioc34/msdata/microtofq/MM8.mzML", head=<unavailable>, result=0x0000000004acc510, runIndex=<unavailable>, config=<unavailable>) const + 948 at DefaultReaderList.cpp:148 
    frame #8: 0x00007f2b01e5d855 mzR.so`pwiz::msdata::ReaderList::read(this=0x00000000058e1170, filename="/software/R_libs/R332_bioc34/msdata/microtofq/MM8.mzML", head="<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\r\n<mzML xmlns=\"http://psi.hupo.org/ms/mzml\" xsi:schemaLocation=\"http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd\" version=\"1.1.0\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\r\n<cvList count=\"2\">\r\n<cv id=\"MS\" fullName=\"Proteomics Standards Initiative Mass Spectrometry Vocabularies\" version=\"2.26.0\" URI=\"http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo\"/>\r\n<cv id=\"UO\" fullName=", result=0x0000000004acc510, sampleIndex=0, config=0x00007ffcdab7cb10) const + 181 at Reader.cpp:101 
    frame #9: 0x00007f2b01eea60f mzR.so`pwiz::msdata::(anonymous namespace)::(filename="/software/R_libs/R332_bioc34/msdata/microtofq/MM8.mzML", msd=0x0000000004acc510, reader=0x00000000058e1170, head="<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\r\n<mzML xmlns=\"http://psi.hupo.org/ms/mzml\" xsi:schemaLocation=\"http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd\" version=\"1.1.0\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">\r\n<cvList count=\"2\">\r\n<cv id=\"MS\" fullName=\"Proteomics Standards Initiative Mass Spectrometry Vocabularies\" version=\"2.26.0\" URI=\"http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo\"/>\r\n<cv id=\"UO\" fullName=")(const string &const, pwiz::msdata::MSData &const, const pwiz::msdata::Reader &const, const string &const) + 127 at MSDataFile.cpp:61 
    frame #10: 0x00007f2b01eec0ba mzR.so`pwiz::msdata::MSDataFile::MSDataFile(this=0x0000000004acc510, filename="/software/R_libs/R332_bioc34/msdata/microtofq/MM8.mzML", reader=<unavailable>, calculateSourceFileChecksum=<unavailable>) + 218 at MSDataFile.cpp:91 
    frame #11: 0x00007f2b01ee434a mzR.so`pwiz::msdata::RAMPAdapter::RAMPAdapter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) [inlined] pwiz::msdata::RAMPAdapter::Impl::Impl(filename="/software/R_libs/R332_bioc34/msdata/microtofq/MM8.mzML", this=0x0000000004acc510) + 5 at RAMPAdapter.cpp:49 
    frame #12: 0x00007f2b01ee4345 mzR.so`pwiz::msdata::RAMPAdapter::RAMPAdapter(this=0x00000000050b8110, filename="/software/R_libs/R332_bioc34/msdata/microtofq/MM8.mzML") + 37 at RAMPAdapter.cpp:296 
    frame #13: 0x00007f2b01d3df7e mzR.so`rampOpenFile(filename="/software/R_libs/R332_bioc34/msdata/microtofq/MM8.mzML") + 542 at ramp.cpp:284 
    frame #14: 0x00007f2b01d3cd15 mzR.so`cRamp::cRamp(this=0x00000000050e4ce0, fileName="/software/R_libs/R332_bioc34/msdata/microtofq/MM8.mzML", declaredScansOnly=<unavailable>) + 149 at cramp.cpp:75 
    frame #15: 0x00007f2b01d45af8 mzR.so`RcppRamp::open(this=0x0000000004fd0ec0, fileName="/software/R_libs/R332_bioc34/msdata/microtofq/MM8.mzML", declaredScansOnly=<unavailable>) + 72 at RcppRamp.cpp:23 
    frame #16: 0x00007f2b01d5a955 mzR.so`Rcpp::CppMethod2<RcppRamp, void, char const*, bool>::operator(this=0x00000000050c9990, object=0x0000000004fd0ec0, args=<unavailable>)(RcppRamp*, SEXPREC**) + 245 at Module_generated_CppMethod.h:215 
    frame #17: 0x00007f2b01d570f0 mzR.so`Rcpp::class_<RcppRamp>::invoke_void(this=<unavailable>, method_xp=<unavailable>, object=0x0000000005cbe020, args=0x00007ffcdab7d2f0, nargs=<unavailable>) + 176 at class.h:212 
    frame #18: 0x00007f2b027e3f41 Rcpp.so`CppMethod__invoke_void(args=<unavailable>) + 449 at Module.cpp:200 
    frame #19: 0x00007f2b26a6e9b1 libR.so`do_External(call=0x000000000570f208, op=0x000000000333ac20, args=0x0000000005dd50b8, env=0x0000000005dd50f0) + 337 at dotcode.c:548 
    frame #20: 0x00007f2b26aa86df libR.so`Rf_eval(e=0x000000000570f208, rho=0x0000000005dd50f0) + 1871 at eval.c:713 
    frame #21: 0x00007f2b26aaadf8 libR.so`do_begin(call=0x000000000570f198, op=0x00000000033254d8, args=0x000000000570f358, rho=0x0000000005dd50f0) + 344 at eval.c:1807 
    frame #22: 0x00007f2b26aa84d1 libR.so`Rf_eval(e=<unavailable>, rho=0x0000000005dd50f0) + 1345 at eval.c:685 
    frame #23: 0x00007f2b26aa9d8d libR.so`Rf_applyClosure(call=<unavailable>, op=<unavailable>, arglist=<unavailable>, rho=<unavailable>, suppliedvars=0x000000000330a1c8) + 1309 at eval.c:1135 
    frame #24: 0x00007f2b26aa82ad libR.so`Rf_eval(e=0x00000000062d0ad8, rho=0x000000000595b3e0) + 797 at eval.c:732 
    frame #25: 0x00007f2b26aaadf8 libR.so`do_begin(call=0x00000000062d0d08, op=0x00000000033254d8, args=0x00000000062d0b10, rho=0x000000000595b3e0) + 344 at eval.c:1807 
    frame #26: 0x00007f2b26aa84d1 libR.so`Rf_eval(e=<unavailable>, rho=0x000000000595b3e0) + 1345 at eval.c:685 
    frame #27: 0x00007f2b26aa84d1 libR.so`Rf_eval(e=<unavailable>, rho=0x000000000595b3e0) + 1345 at eval.c:685 
    frame #28: 0x00007f2b26aaadf8 libR.so`do_begin(call=0x00000000062d04a0, op=0x00000000033254d8, args=0x00000000062d0e90, rho=0x000000000595b3e0) + 344 at eval.c:1807 
    frame #29: 0x00007f2b26aa84d1 libR.so`Rf_eval(e=<unavailable>, rho=0x000000000595b3e0) + 1345 at eval.c:685 
    frame #30: 0x00007f2b26aa9d8d libR.so`Rf_applyClosure(call=<unavailable>, op=<unavailable>, arglist=<unavailable>, rho=<unavailable>, suppliedvars=0x000000000330a1c8) + 1309 at eval.c:1135 
    frame #31: 0x00007f2b26aa82ad libR.so`Rf_eval(e=0x000000000595a9f0, rho=0x000000000334ff58) + 797 at eval.c:732 
    frame #32: 0x00007f2b26aabf66 libR.so`do_set(call=0x000000000595b680, op=0x000000000330c2d8, args=<unavailable>, rho=0x000000000334ff58) + 166 at eval.c:2197 
    frame #33: 0x00007f2b26aa84d1 libR.so`Rf_eval(e=<unavailable>, rho=0x000000000334ff58) + 1345 at eval.c:685 
    frame #34: 0x00007f2b26acf932 libR.so`Rf_ReplIteration(rho=0x000000000334ff58, savestack=<unavailable>, browselevel=<unavailable>, state=0x00007ffcdab7f020) + 546 at main.c:258 
    frame #35: 0x00007f2b26acfca1 libR.so`R_ReplConsole(rho=0x000000000334ff58, savestack=0, browselevel=0) + 129 at main.c:308 
    frame #36: 0x00007f2b26acfd58 libR.so`run_Rmainloop + 72 at main.c:1059 
    frame #37: 0x0000000000d85dc2 rsession`rstudio::r::session::runEmbeddedR(rstudio::core::FilePath const&, rstudio::core::FilePath const&, bool, bool, SA_TYPE, rstudio::r::session::Callbacks const&, rstudio::r::session::InternalCallbacks*) + 434 
    frame #38: 0x0000000000d6791d rsession`rstudio::r::session::run(rstudio::r::session::ROptions const&, rstudio::r::session::RCallbacks const&) + 9581 
    frame #39: 0x00000000006a7299 rsession`main + 10809 
    frame #40: 0x00007f2b2530e830 libc.so.6`__libc_start_main(main=(rsession`main), argc=11, argv=0x00007ffcdab81fd8, init=<unavailable>, fini=<unavailable>, rtld_fini=<unavailable>, stack_end=0x00007ffcdab81fc8) + 240 at libc-start.c:291 
    frame #41: 0x00000000006b4fe1 rsession`_start + 41 

間違いなく次のようになります。付属のlldbで実行

library(mzR) 
library(msdata) 

mzxml <- system.file("threonine/threonine_i2_e35_pH_tree.mzXML", 
        package = "msdata") 
aa <- openMSfile(mzxml) # this works 

mzml <- system.file("microtofq/MM8.mzML", package = "msdata") 

bb <- openMSfile(mzml) # this crashes R, but only in RStudio 

sessionInfo() 

> sessionInfo() 
R version 3.3.2 (2016-10-31) 
Platform: x86_64-pc-linux-gnu (64-bit) 
Running under: Ubuntu 16.04.1 LTS 

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  

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

other attached packages: 
[1] msdata_0.14.0 mzR_2.8.1  Rcpp_0.12.9 

loaded via a namespace (and not attached): 
[1] ProtGenerics_1.6.0 parallel_3.3.2  Biobase_2.34.0  
[4] codetools_0.2-15 BiocGenerics_0.20.0 

更新

（！方法により、ルートとしてそれを実行することを確認してください）は、以下のスタックトレースを与えますProteowizard側でメモリの問題が発生しましたが、それはちょうどベースのRプロセスで無視されます。

Answer 1

消毒剤を使用してコンパイルRのバージョンでこれを実行しているとき、私は以下を参照してください

特に

> source("msdata.R", echo = TRUE) 

> library(mzR) 
Loading required package: Rcpp 

> library(msdata) 

> mzxml <- system.file("threonine/threonine_i2_e35_pH_tree.mzXML", 
+      package = "msdata") 

> aa <- openMSfile(mzxml) # this works 
ramp.cpp:1197:34: runtime error: index -1 out of bounds for type 'char [513]' 
SUMMARY: AddressSanitizer: undefined-behavior ramp.cpp:1197:34 in 

> mzml <- system.file("microtofq/MM8.mzML", package = "msdata") 

> bb <- openMSfile(mzml) # this crashes R, but only in RStudio 

、このビットを：

> aa <- openMSfile(mzxml) # this works 
ramp.cpp:1197:34: runtime error: index -1 out of bounds for type 'char [513]' 
SUMMARY: AddressSanitizer: undefined-behavior ramp.cpp:1197:34 in 

はopenMSfile()機能と間違って行く何かがあるかもしれない意味 - 無効なオフセットでデータを読み取ろうとしているようです。私はmzRの保守担当者にこの問題を提出します。

---

> sessionInfo() 
R Under development (unstable) (2017-01-17 r72002) 
Platform: x86_64-apple-darwin16.3.0 (64-bit) 
Running under: macOS Sierra 10.12.2 

locale: 
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 

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

other attached packages: 
[1] msdata_0.15.0  mzR_2.9.3   Rcpp_0.12.9 
[4] testthat_1.0.2  rmarkdown_1.3  knitr_1.15.1 
[7] roxygen2_5.0.1  devtools_1.12.0.9000 

loaded via a namespace (and not attached): 
[1] magrittr_1.5  BiocGenerics_0.21.3 pkgload_0.0.0.9000 
[4] R6_2.2.0   stringr_1.1.0  tools_3.4.0 
[7] pkgbuild_0.0.0.9000 parallel_3.4.0  Biobase_2.35.0 
[10] withr_1.0.2   htmltools_0.3.5  ProtGenerics_1.7.0 
[13] rprojroot_1.2  digest_0.6.11  crayon_1.3.2 
[16] codetools_0.2-15 memoise_1.0.0  evaluate_0.10 
[19] stringi_1.1.2  compiler_3.4.0  backports_1.0.5 

---

編集：ここでRを構築するために使用されるのconfigureコールがあります。すべてのビルドされたパッケージに同じコンパイラ+フラグが使用されます。 （R.home("etc/Makeconf")から抽出された）

# R was configured using the following call 
# (not including env. vars and site configuration) 
# configure '--with-blas=-L/usr/local/opt/openblas/lib -lopenblas' '--with-lapack=-L/usr/local/opt/lapack/lib -llapack' '--with-cairo' '--disable-R-framework' '--enable-R-shlib' '--with-readline' '--enable-R-profiling' '--enable-memory-profiling' '--with-valgrind-instrumentation=2' '--without-internal-tzcode' '--prefix=/Users/kevin/r/r-devel-sanitizers' 'PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig' 

CC = clang-3.9 -std=gnu99 -fsanitize=address,undefined -fno-omit-frame-pointer -fno-sanitize=float-divide-by-zero 
CXX = clang++-3.9 -fsanitize=address,undefined -fno-omit-frame-pointer -fno-sanitize=float-divide-by-zero 

---

EDITのV2：lldbスタックトレースを考えると、それは確かにブーストのバージョン（バージョンによって使用される対RStudioで使用されるバンドルされたバージョン間の衝突かもしれ犯人のように見えますmzR）。 mzRは、rsessionの実行可能ファイル内のブーストルーチンを誤って呼び出している可能性があることに注意してください。