R session aborted using R studio

[mtk]

Hi all,

I am using a script which mostly uses the xcms package and every time a run the script in R studio R shuts down and I get an error message saying that R session has aborted and I need to restart the session. I have tried uninstalling R and reinstalling and even tried on a computer with more RAM but I still get the same error. I have the diagnostic report here below.
Happy for any suggestions on what is going wrong.

Thanks.

$UATDATA
[1] "C:\\WINDOWS\\CCM\\UATData\\D9F8C395-CAB8-491d-B8AC-179A1FE1BE77"

$USERDNSDOMAIN
[1] "IC.AC.UK"

$USERDOMAIN
[1] "IC"

$USERDOMAIN_ROAMINGPROFILE
[1] "IC"

$USERNAME
[1] "mtk616"

$USERPROFILE
[1] "C:\\Users\\mtk616"

$VBOX_MSI_INSTALL_PATH
[1] "C:\\Program Files\\Oracle\\VirtualBox\\"

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

 [1] ".GlobalEnv"        "tools:rstudio"     "package:stats"     "package:graphics"  "package:grDevices"
 [6] "package:utils"     "package:datasets"  "package:methods"   "Autoloads"         "package:base"     
Log file: rdesktop.log
--------------------------------------------------

12 Mar 2018 17:45:06 [rdesktop] ERROR system error 231 (All pipe instances are busy); 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
12 Mar 2018 17:45:06 [rdesktop] ERROR system error 231 (All pipe instances are busy); 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
20 Mar 2018 16:16:55 [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
02 May 2018 10:29:27 [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
02 May 2018 10:29:37 [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
02 May 2018 11:02:43 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: rstudio::core::Error rstudio::core::system::ChildProcess::run() C:\Users\Administrator\rstudio\src\cpp\core\system\Win32ChildProcess.cpp:521; LOGGED FROM: void rstudio::desktop::openUrl(const QUrl&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopUtils.cpp:307

Log file: rsession-mtk616.log
--------------------------------------------------

02 May 2018 08:55:42 [rsession-mtk616] ERROR system error 67 (The network name cannot be found) [path=//icnas3.cc.ic.ac.uk/DESCRIPTION]; OCCURRED AT: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325; LOGGED FROM: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325
02 May 2018 08:55:42 [rsession-mtk616] ERROR system error 67 (The network name cannot be found) [path=//icnas3.cc.ic.ac.uk/Asthma.NPC.MS.data/Converted data/RPOS/DESCRIPTION]; OCCURRED AT: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325; LOGGED FROM: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325
02 May 2018 08:55:43 [rsession-mtk616] ERROR system error 67 (The network name cannot be found) [path=//icnas3.cc.ic.ac.uk/DESCRIPTION]; OCCURRED AT: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325; LOGGED FROM: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325
02 May 2018 08:55:43 [rsession-mtk616] ERROR system error 67 (The network name cannot be found) [path=//icnas3.cc.ic.ac.uk/Asthma.NPC.MS.data/Converted data/RPOS/DESCRIPTION]; OCCURRED AT: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325; LOGGED FROM: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325
02 May 2018 08:59:24 [rsession-mtk616] ERROR system error 67 (The network name cannot be found) [path=//icnas3.cc.ic.ac.uk/DESCRIPTION]; OCCURRED AT: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325; LOGGED FROM: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325
02 May 2018 08:59:24 [rsession-mtk616] ERROR system error 67 (The network name cannot be found) [path=//icnas3.cc.ic.ac.uk/Asthma.NPC.MS.data/Converted data/RPOS/DESCRIPTION]; OCCURRED AT: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325; LOGGED FROM: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325
02 May 2018 10:05:40 [rsession-mtk616] ERROR system error 67 (The network name cannot be found) [path=//icnas3.cc.ic.ac.uk/DESCRIPTION]; OCCURRED AT: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325; LOGGED FROM: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325
02 May 2018 10:32:32 [rsession-mtk616] WARNING Process supervisor did not terminate within 1 second; LOGGED FROM: void {anonymous}::rCleanup(bool) C:\Users\Administrator\rstudio\src\cpp\session\SessionMain.cpp:1099
02 May 2018 10:32:39 [rsession-mtk616] WARNING Process supervisor did not terminate within 1 second; LOGGED FROM: void {anonymous}::rCleanup(bool) C:\Users\Administrator\rstudio\src\cpp\session\SessionMain.cpp:1099
02 May 2018 11:50:22 [rsession-mtk616] ERROR system error 109 (The pipe has been ended); OCCURRED AT: virtual void rstudio::session::NamedPipeHttpConnection::close() C:\Users\Administrator\rstudio\src\cpp\session\http\SessionNamedPipeHttpConnectionListener.hpp:198; LOGGED FROM: virtual void rstudio::session::NamedPipeHttpConnection::close() C:\Users\Administrator\rstudio\src\cpp\session\http\SessionNamedPipeHttpConnectionListener.hpp:198
03 May 2018 09:53:46 [rsession-mtk616] WARNING Abort requested; LOGGED FROM: bool rstudio::session::connection::checkForAbort(rstudio_boost::shared_ptr<rstudio::session::HttpConnection>, rstudio_boost::function<void()>) C:\Users\Administrator\rstudio\src\cpp\session\http\SessionHttpConnectionUtils.cpp:137
03 May 2018 12:39:09 [rsession-mtk616] ERROR system error 67 (The network name cannot be found) [path=//icnas3.cc.ic.ac.uk/DESCRIPTION]; OCCURRED AT: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325; LOGGED FROM: bool rstudio::core::FilePath::exists() const C:\Users\Administrator\rstudio\src\cpp\core\FilePath.cpp:325

[mara]

Does this happen if you try to run the same script outside of the the RStudio IDE?

For clarification about the difference between R and RStudio, I made this little FAQ:

Differentiating R from RStudio

Aside: goals for this thread

I'm hoping this will help people disambiguate R from RStudio, and also help with getting questions in the right category. This is a bit of a mashup of the times I've tried to explain this in individual threads, so please feel free to add to this topic for further clarification/point out corrections, etc.

Before putting a code-related question in the #rstudio-ide category or using the rstudio tag, it's helpful to ask yourself: Does this work in the regular R GUI, but not when you're in RStudio? If you're using RStudio, you're using R — RStudio is just an IDE (Integrated Development Environment) in which you are using the R language. (On of my favourite fi…

[shawn]

Hi mtk!

You might try closing RStudio and delete the following files:

1. C: > users > username > AppData > Local > RStudio-Desktop
2. C: > users > username > AppData > Roaming > RStudio

Dive back into RStudio. (No restart required.)

Logic: The causes and symptoms can vary, but clearing these files flushes the program - data (working files) saved elsewhere will remain.

Enjoy!

shawn