Fatal error on regex or stringr

General
, ,
1

I am encountering a fatal error with any attempt to perform a regex function. Or, at least this is one source of fatal errors, they might be more broad than this. Minimal example:

library(stringr)
str_detect("stuffaboutstuff", "ab")

(code edited for typo)

I'm sure I broke something in my installation recently by trying to install bioconductor packages. I was getting conflicts, and so cleaned up folders of old packages (moved R 3.3 and 3.4 win-library to 3.5 and ran update, deleted PATH R_user_libs to the 3.3 and 3.4 directories) which eventually got me past the problem. I don't have an .RData file to delete (set to never save or restore .RData in global options). I just need some ideas to direct my troubleshooting more.

Running R 3.5.1, Rstudio 1.1.463 on Windows 10.

Diagnostic report:

[1] "1.1.463"

$R
[1] "C:\\PROGRA~1\\R\\R-35~1.1\\bin\\x64\\R.exe"

$pdflatex
[1] "C:\\PROGRA~1\\MIKTEX~1.9\\miktex\\bin\\x64\\pdflatex.exe"

$bibtex
[1] "C:\\PROGRA~1\\MIKTEX~1.9\\miktex\\bin\\x64\\bibtex.exe"

$gcc
[1] ""

$git
[1] "C:\\PROGRA~1\\Git\\cmd\\git.exe"

$svn
[1] ""

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1    yaml_2.2.0    

SysInfo:
       sysname        release        version       nodename        machine          login           user effective_user 
     "Windows"     ">= 8 x64"   "build 9200"        "ORUAL"       "x86-64"        "blaze"        "blaze"        "blaze" 

R Version:
               _                           
platform       x86_64-w64-mingw32          
arch           x86_64                      
os             mingw32                     
system         x86_64, mingw32             
status                                     
major          3                           
minor          5.1                         
year           2018                        
month          07                          
day            02                          
svn rev        74947                       
language       R                           
version.string R version 3.5.1 (2018-07-02)
nickname       Feather Spray               
$ALLUSERSPROFILE
[1] "C:\\ProgramData"

$APPDATA
[1] "C:\\Users\\blaze\\AppData\\Roaming"

$CLICOLOR_FORCE
[1] "1"

$CommonProgramFiles
[1] "C:\\Program Files\\Common Files"

$`CommonProgramFiles(x86)`
[1] "C:\\Program Files (x86)\\Common Files"

$CommonProgramW6432
[1] "C:\\Program Files\\Common Files"

$COMPUTERNAME
[1] "ORUAL"

$ComSpec
[1] "C:\\WINDOWS\\system32\\cmd.exe"

$CUDA_PATH_V9_0
[1] "C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v9.0"

$cuDNN_bin_PATH
[1] "C:\\Program Files\\NVIDIA GPU Computing Toolkit\\cudnn-9.0-windows10-x64-v7.4.1.5\\cuda\\bin\\"

$CUPTI_v9_PATH
[1] "C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v9.0\\extras\\CUPTI\\libx64"

$DISPLAY
[1] ":0"

$DriverData
[1] "C:\\Windows\\System32\\Drivers\\DriverData"

$FPS_BROWSER_APP_PROFILE_STRING
[1] "Internet Explorer"

$FPS_BROWSER_USER_PROFILE_STRING
[1] "Default"

$GFORTRAN_STDERR_UNIT
[1] "-1"

$GFORTRAN_STDOUT_UNIT
[1] "-1"

$HOME
[1] "C:/Users/blaze/Documents"

$HOMEDRIVE
[1] "C:"

$HOMEPATH
[1] "\\Users\\blaze"

$JAVA_HOME
[1] "C:\\Program Files\\Java\\jdk1.8.0_181"

$LOCALAPPDATA
[1] "C:\\Users\\blaze\\AppData\\Local"

$LOGONSERVER
[1] "\\\\ORUAL"

$MSYS2_ENV_CONV_EXCL
[1] "R_ARCH"

$NUMBER_OF_PROCESSORS
[1] "8"

$NVCUDASAMPLES9_0_ROOT
[1] "C:\\ProgramData\\NVIDIA Corporation\\CUDA Samples\\v9.0"

$NVTOOLSEXT_PATH
[1] "C:\\Program Files\\NVIDIA Corporation\\NvToolsExt\\"

$OneDrive
[1] "C:\\Users\\blaze\\OneDrive"

$OS
[1] "Windows_NT"

$PATH
[1] "C:\\Program Files\\R\\R-3.5.1\\bin\\x64;C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v9.0\\bin;C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v9.0\\libnvvp;C:\\Rtools\\bin;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath;C:\\Perl64\\site\\bin;C:\\Perl64\\bin;C:\\ProgramData\\Oracle\\Java\\javapath;C:\\Program Files (x86)\\Razer Chroma SDK\\bin;C:\\Program Files\\Razer Chroma SDK\\bin;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\Users\\Administrator\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Program Files\\MiKTeX 2.9\\miktex\\bin\\x64\\;C:\\Program Files\\Git\\cmd;C:\\Program Files\\MySQL\\MySQL Utilities 1.6\\;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files\\PuTTY\\;C:\\Program Files (x86)\\ClustalW2\\;C:\\WINDOWS\\System32\\OpenSSH\\;C:\\Program Files\\Microsoft VS Code\\bin;C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v9.0;C:\\Program Files\\NVIDIA GPU Computing Toolkit\\cudnn-9.0-windows10-x64-v7.4.1.5\\cuda\\bin\\;C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v9.0\\extras\\CUPTI\\libx64;C:\\Users\\blaze\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\blaze\\AppData\\Local\\atom\\bin;C:\\Users\\blaze\\AppData\\Local\\Microsoft\\WindowsApps;C:\\Users\\blaze\\AppData\\Local\\GitHubDesktop\\bin;C:\\Users\\blaze\\AppData\\Local\\Programs\\MiKTeX 2.9\\miktex\\bin\\x64\\;C:\\Program Files\\Maven\\apache-maven-3.5.4\\bin;C:\\Users\\blaze\\Anaconda3;C:\\Users\\blaze\\Anaconda3\\Scripts;"

$PATHEXT
[1] ".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC;.DLL"

$PROCESSOR_ARCHITECTURE
[1] "AMD64"

$PROCESSOR_IDENTIFIER
[1] "Intel64 Family 6 Model 94 Stepping 3, GenuineIntel"

$PROCESSOR_LEVEL
[1] "6"

$PROCESSOR_REVISION
[1] "5e03"

$ProgramData
[1] "C:\\ProgramData"

$ProgramFiles
[1] "C:\\Program Files"

$`ProgramFiles(x86)`
[1] "C:\\Program Files (x86)"

$ProgramW6432
[1] "C:\\Program Files"

$PSModulePath
[1] "C:\\Program Files\\WindowsPowerShell\\Modules;C:\\WINDOWS\\system32\\WindowsPowerShell\\v1.0\\Modules"

$PUBLIC
[1] "C:\\Users\\Public"

$Python3
[1] "C:\\Users\\blaze\\Anaconda3;C:\\Users\\blaze\\Anaconda3\\Scripts"

$R_ARCH
[1] "/x64"

$R_COMPILED_BY
[1] "gcc 4.9.3"

$R_DOC_DIR
[1] "C:/PROGRA~1/R/R-35~1.1/doc"

$R_HOME
[1] "C:/PROGRA~1/R/R-35~1.1"

$R_LIBS_USER
[1] "C:\\Program Files\\R\\R-3.5.1;C:\\Users\\blaze\\Documents\\R\\win-library\\3.5;C:\\Program Files\\R\\R-3.5.1\\library;"

$R_USER
[1] "C:/Users/blaze/Documents"

$RMARKDOWN_MATHJAX_PATH
[1] "C:/Program Files/RStudio/resources/mathjax-26"

$RS_LOCAL_PEER
[1] "\\\\.\\pipe\\40294-rsession"

$RS_RPOSTBACK_PATH
[1] "C:/Program Files/RStudio/bin/rpostback"

$RS_SHARED_SECRET
[1] "63341846741"

$RSTUDIO
[1] "1"

$RSTUDIO_CONSOLE_COLOR
[1] "256"

$RSTUDIO_CONSOLE_WIDTH
[1] "80"

$RSTUDIO_MSYS_SSH
[1] "C:/Program Files/RStudio/bin/msys-ssh-1000-18"

$RSTUDIO_PANDOC
[1] "C:/Program Files/RStudio/bin/pandoc"

$RSTUDIO_SESSION_PORT
[1] "40294"

$RSTUDIO_USER_IDENTITY
[1] "blaze"

$RSTUDIO_WINUTILS
[1] "C:/Program Files/RStudio/bin/winutils"

$SESSIONNAME
[1] "Console"

$SystemDrive
[1] "C:"

$SystemRoot
[1] "C:\\WINDOWS"

$TEMP
[1] "C:\\Users\\blaze\\AppData\\Local\\Temp"

$TERM
[1] "xterm-256color"

$TMP
[1] "C:\\Users\\blaze\\AppData\\Local\\Temp"

$USERDOMAIN
[1] "ORUAL"

$USERDOMAIN_ROAMINGPROFILE
[1] "ORUAL"

$USERNAME
[1] "blaze"

$USERPROFILE
[1] "C:\\Users\\blaze"

$windir
[1] "C:\\WINDOWS"

 [1] ".GlobalEnv"        "tools:rstudio"     "package:stats"     "package:graphics"  "package:grDevices" "package:utils"     "package:datasets" 
 [8] "package:methods"   "Autoloads"         "package:base"

last rdesktop.log event:

12 Dec 2018 21:12:55 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288

last rsession.log event:

12 Dec 2018 21:12:33 [rsession-blaze] CLIENT EXCEPTION (rsession-blaze): (TypeError) : undefined is not an object (evaluating 'this.a.a.r.row');|||com/google/gwt/dev/jjs/intrinsic/com/google/gwt/lang/Exceptions.java#28::wrap|||com/google/gwt/core/client/impl/SchedulerImpl.java#167::runScheduledTasks|||com/google/gwt/core/client/impl/SchedulerImpl.java#338::flushPostEventPumpCommands|||com/google/gwt/core/client/impl/SchedulerImpl.java#76::execute|||com/google/gwt/core/client/impl/SchedulerImpl.java#140::execute|||com/google/gwt/core/client/impl/Impl.java#244::apply|||com/google/gwt/core/client/impl/Impl.java#283::entry0|||#-1::anonymous|||com/google/gwt/cell/client/AbstractEditableCell.java#41::viewDataMap|||Client-ID: 33e600bb-c1b1-46bf-b562-ab5cba070b0e|||User-Agent: Mozilla/5.0 (Windows NT 6.2  WOW64) AppleWebKit/538.1 (KHTML, like Gecko) rstudio Safari/538.1 Qt/5.4.1
2

Not that it should crash your IDE, but if this is the exact code you're running, you are missing a quotation mark after ab…

library(stringr)
str_detect("stuffaboutstuff", "ab")
#> [1] TRUE

Created on 2018-12-13 by the reprex package (v0.2.1.9000)

3

Good catch, but yeah that was just a typo on my part writing the post. The marks were correct in Rstudio (just confirmed it still crashes)

4

Probably should have tested this earlier, but this also crashes R outside of Rstudio. So it's not an IDE problem, it's a I broke my everything problem. Should I look to remove everything and start over? And how would I start that?

5

I can't quite tell from what you have above (n.b. you can format code by surrounding it with three backticks in the line above and below — it's easier to read, and also will mean you don't end up with a computer emoji in the middle of the log), but if you haven't included a crash report, you may want to get that as well

6

But Mara, if I used backticks I wouldn't have gotten my first emoji badge!

Original post updated with better formatting, I managed to find/generate a crash dump but I'm not allowed to upload it (non-approved file type) and when I open it in Atom it doesn't parse as text. This google drive link should work (two dumps, one from Rgui one from rstudio).

Thanks so much for your help Mara!

1 Like
7

Nice. I'm not an IDE dev (I'm more likely to understand log files entirely in emoji), but I'm guessing we can get someone more informed (read: almost anyone) to take a look. :slightly_smiling_face:

8

If I understand things correctly, it sounds like you run a really simple function in R, and R crashes. Also, those dmp files are 30MB, so that's not really something many folks will dive into.

I'd suggest following the advice in the RStudio Crashed troubleshooting guide mara referenced. With an uninstall reinstall of R.

9

Thanks Curtis, I was starting to figure this was the eventual route I would need to take, just wasn't sure if the problem would ring any bells for other people. I'm just getting over a bout of sickness that kept me from troubleshooting these last few days, but I'll be going with a clean reinstall tomorrow.

10

Uninstalling and reinstalling R + Rstudio did not resolve my issue. However going a step further and deleting my R package libraries (user/documents/R/win-library) and all R_libs_user environment variables, then reinstalling R/Rstudio fixed the problem. It was a bit scorched earth but I'm just glad to have a working install again. Thanks all!

11

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