RStudio 1.1.372 and projects


#1

Hi, I’m not sure what the distinction is between posting here and on the RStudio support site, but hopefully this is an appropriate post. I have found that when I use the 1.1.x preview versions of RStudio, it crashes when I attempt to load a project. This has never been an issue with previous versions. I’ve noticed that there are several posts on the RStudio support site (including one from me) that report similar issues, but none of them have had a response yet. I supplied log files, etc on the support site, so I’m loathe to do the same here as it may not be appropriate, but it would be good to know if others are having similar problems and also whether this is a known issue that is being worked on. And also whether there are any workarounds. I’ve had to go back to the current stable version, which is a shame as there are some nice features of 1.1.x that I would like to use.

Thanks,
David


Sessions was terminated - message
#2

Can you provide a link to your support post, and/or give the details such as environment and error message here? It will make it easier to narrow down what the potential sources of the problem are.


#3

Thanks for fast response! I get different error messages. Just to be clear, these occur after attempting to load a package, not on startup of RStudio The first one is a JavaScript Alert that reads “R encountered a fatal error. The session was terminated.” The second one is “R Session Aborted, R encountered a fatal error. The session was terminated.” There is a Start New Session button below the message, but the same error just reoccurs when I click on it. I’ve also noticed that the Files and Packages panes are empty. I’m using R 3.4.1 and Windows 7. Below I’ve added today’s entries in the log file:and the diagnostics report.

Thanks for your help.
David

22 Sep 2017 16:07:33 [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
22 Sep 2017 16:07:43 [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
22 Sep 2017 16:07:53 [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
22 Sep 2017 16:08:00 [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
22 Sep 2017 16:09:55 [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
22 Sep 2017 16:12:29 [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
22 Sep 2017 16:12:39 [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
22 Sep 2017 16:12:49 [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
22 Sep 2017 16:12:53 [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
22 Sep 2017 16:13:02 [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
22 Sep 2017 16:13:12 [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
22 Sep 2017 16:13:22 [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
22 Sep 2017 16:13:32 [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
22 Sep 2017 16:13:42 [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
22 Sep 2017 16:13:51 [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
22 Sep 2017 16:13:52 [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
22 Sep 2017 16:14:03 [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
22 Sep 2017 16:14:13 [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
22 Sep 2017 16:14:23 [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
22 Sep 2017 16:14:33 [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
22 Sep 2017 16:14:43 [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
22 Sep 2017 16:14:53 [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

This is the diagnostics report:
[1] “1.1.372”

$R
[1] “C:\PROGRA~1\R\R-34~1.1\bin\x64\R.exe”

$pdflatex
[1] “C:\PROGRA~2\MIKTEX~1.9\miktex\bin\pdflatex.exe”

$bibtex
[1] “C:\PROGRA~2\MIKTEX~1.9\miktex\bin\bibtex.exe”

$gcc
[1] “c:\Rtools\GCC-46~1.3\bin\gcc.exe”

$git
[1] “”

$svn
[1] “”

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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

loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1 yaml_2.1.14

SysInfo:
sysname release version
"Windows" “7 x64” “build 7601, Service Pack 1"
nodename machine login
"SBS-PL400841FA” “x86-64” “dbarron"
user effective_user
"dbarron” “dbarron”

R Version:
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 4.1
year 2017
month 06
day 30
svn rev 72865
language R
version.string R version 3.4.1 (2017-06-30)
nickname Single Candle
$__COMPAT_LAYER
[1] “ElevateCreateProcess”

$ALLUSERSPROFILE
[1] “C:\ProgramData”

$APPDATA
[1] “C:\Users\dbarron\AppData\Roaming”

$asl.log
[1] “Destination=file”

$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] “SBS-PL400841FA”

$ComSpec
[1] “C:\Windows\system32\cmd.exe”

$DellClientSystemUpdatePath
[1] “C:\Program Files (x86)\Dell\ClientSystemUpdate\”

$DISPLAY
[1] “:0”

$FP_NO_HOST_CHECK
[1] “NO”

$GFORTRAN_STDERR_UNIT
[1] “-1”

$GFORTRAN_STDOUT_UNIT
[1] “-1”

$HOME
[1] “C:/Users/dbarron/Documents”

$HOMEDRIVE
[1] “C:”

$HOMEPATH
[1] “\Users\dbarron”

$LOCALAPPDATA
[1] “C:\Users\dbarron\AppData\Local”

$LOGONSERVER
[1] “\\SBS-CL019101”

$MOZ_PLUGIN_PATH
[1] “C:\Program Files\Tracker Software\PDF Viewer\Win32\”

$NUMBER_OF_PROCESSORS
[1] “4”

$OS
[1] “Windows_NT”

$PATH
[1] “C:\Program Files\R\R-3.4.1\bin\x64;c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files (x86)\MiKTeX 2.9\miktex\bin\;C:\Program Files\Intel\Intel® Management Engine Components\DAL;C:\Program Files\Intel\Intel® Management Engine Components\IPT;C:\Program Files (x86)\Intel\Intel® Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel® Management Engine Components\IPT;C:\Program Files\cURL\bin;C:\Python34;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files (x86)\Skype\Phone\”

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

$PROCESSOR_ARCHITECTURE
[1] “AMD64”

$PROCESSOR_IDENTIFIER
[1] “Intel64 Family 6 Model 69 Stepping 1, GenuineIntel”

$PROCESSOR_LEVEL
[1] “6”

$PROCESSOR_REVISION
[1] “4501”

$ProgramData
[1] “C:\ProgramData”

$ProgramFiles
[1] “C:\Program Files”

$ProgramFiles(x86)
[1] “C:\Program Files (x86)”

$ProgramW6432
[1] “C:\Program Files”

$PSModulePath
[1] “C:\Windows\system32\WindowsPowerShell\v1.0\Modules\”

$PUBLIC
[1] “C:\Users\Public”

$PYTHONPATH
[1] “%PYTHONPATH%;C:\Python34;C:\Python34;C:\Python34”

$R_ARCH
[1] “/x64”

$R_COMPILED_BY
[1] “gcc 4.9.3”

$R_DOC_DIR
[1] “C:/PROGRA~1/R/R-34~1.1/doc”

$R_HOME
[1] “C:/PROGRA~1/R/R-34~1.1”

$R_LIBS_USER
[1] “C:/Users/dbarron/Documents/R/win-library/3.4”

$R_USER
[1] “C:/Users/dbarron/Documents”

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

$RS_LOCAL_PEER
[1] “\\.\pipe\33996-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] “33996”

$RSTUDIO_USER_IDENTITY
[1] “dbarron”

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

$SESSIONNAME
[1] “Console”

$SystemDrive
[1] “C:”

$SystemRoot
[1] “C:\Windows”

$TEMP
[1] “C:\Users\dbarron\AppData\Local\Temp”

$TERM
[1] “xterm-256color”

$TMP
[1] “C:\Users\dbarron\AppData\Local\Temp”

$TWFY_API_KEY
[1] “Fq3xvFCDep2LDSwFPrGFXBv2”

$TWITTER_PAT
[1] “C:/Users/dbarron/Documents//twitter_token.rds”

$UOIPME_REG_PATH
[1] “C:\Program Files\Intel Corporation\USB over IP”

$USERDNSDOMAIN
[1] “SBS.OX.AC.UK

$USERDOMAIN
[1] “SBS”

$USERNAME
[1] “dbarron”

$USERPROFILE
[1] “C:\Users\dbarron”

$windir
[1] “C:\Windows”

$windows_tracing_flags
[1] “3”

$windows_tracing_logfile
[1] “C:\BVTBin\Tests\installpackage\csilogfile.log”

[1] “.GlobalEnv” “tools:rstudio” “package:stats” “package:graphics”
[5] “package:grDevices” “package:utils” “package:datasets” “package:methods”
[9] “Autoloads” "package:base"
Log file: rdesktop.log


#4

You aren’t alone! This is also happening to me. I don’t have my computer with me now, so I can’t provide a log, but I’m glad you did. I love 1.1 and can’t wait for all the bugs to get fixed.


#5

Hello,

Yes, that also happened to me in a Windows box, although also happens in OSX.
The bug was present already in an earlier version.
I reported to support, here is the link:

Thanks,
Carlos.


#6

It looks like this is likely an issue caused by attempting to use RStudio with a project being managed by Dropbox. Unfortunately, this can lead to race conditions where RStudio and Dropbox both attempt to access a file at the same time, and if RStudio ‘loses’ that race then it will report an error. (This sort of issue is seen with other cloud-synchronization services as well; e.g. Google Cloud or Microsoft OneDrive.)

RStudio will store its project-specific session state within a hidden folder in the project directory, called .Rproj.user. You might try telling Dropbox to ignore that folder. While this implies that your project-specific settings won’t be synchronized by Dropbox, it should at least work around this issue.


#7

Thanks Kevin. I’d already seen that flagged as a possible issue, and while I thought it was unlikely to be the cause given that I’d never had similar problems with earlier versions of RStudio, I did make sure by testing with projects not on Dropbox, and had exactly the same problems. In fact even when I try to create a brand new project I still get the “JavaScript Alert 127.0.0.1 R Encountered a fatal error. The session was terminated” error message.

I’m not sure if this is relevant, but I’ve noticed that sometimes (but not consistently) I get the same error when a project isn’t loaded but I attempt access the Packages pane.

Thanks,
David


#8

I wonder if something is going wrong on startup while RStudio attempts to crawl your R library?

Can you share the output of list.files(.libPaths(), full.names = TRUE)?

I’d also be curious whether explicitly disabling the package’s pane makes a difference – see the first checkbox in the Tools -> Global Options... -> Packages preferences pane:


#9

output is in this gist:

https://gist.github.com/dnbarron/427693ec73a8d8591bc7695fef2721d2

I tried disabling the packages pane, but it had no effect.

Thanks for your help!


#10

The only vaguely suspicious thing I see there is what are likely temporary directories:

[205] "C:/Users/dbarron/Documents/R/win-library/3.4/filebac3abd5cb2"     
[206] "C:/Users/dbarron/Documents/R/win-library/3.4/filebc479c27a0d"     

You might want to clean those up, although it seems unlikely that they would be the culprit here.


#11

Yes, you’re right, sadly!


#12

@kevinushey Hi Kevin,

I’ve a feeling at least some of the issues might be related to Git. Using both git and dropbox is probably not a smart idea anyway! However, fiddling around with some of my projects, I’ve found that deleting the local git repo seems to solve most (but not all) of the crashes. I know RStudio 1.1 has made some changes to the git interface, so does that seem plausible?

Update When I initialise a new git repo from within RStudio in a project not on dropbox I get the same issues as before, even when the project worked without any problems before the repo was created. So, it looks like a git issue, but not an issue with an interaction between git and dropbox.


#13

@DavidB We’ve just released a new version of the preview, 1.1.379, which we believe will fix the “R encountered a fatal error” issue you’ve seen. Would you be willing to download it and let us know if it fixes the problem for you?

https://www.rstudio.com/products/rstudio/download/preview/


#14

@jonathan Thanks for letting me know. I’ve downloaded it, and so far it’s looking good! So happy to be able to use your great new version. I’ll carry on testing it and let you know if there are any more problems.

Thanks again!


#15

So I’ve been using 1.1.379 for a few days now, and had no issues at all. The new features are all great, especially the terminal and the object viewer for lists. Thanks for your help with this.


#16

Great, happy to hear everything’s working well! Let us know if you run into any more trouble.