我一直在这个问题上玩了好几个小时，我想我终于可以重现它了。Rstudio rsession在编辑文件时挂起

当我开始新的Rstudio会话时，一切正常，没有问题。我甚至可以加载对象并执行代码。

编辑当前文件时出现问题。只要我编辑文件，我不能再执行命令，当我通过top查看CPU使用情况时，它显示rsession正在使用100％的CPU，并且它永不停止。在此期间，我可以继续编辑该文件，并且Rstudio GUI显示工作正常，但代码执行已冻结。我也无法保存文件。

编辑：我试图编辑的文档类型是.Rmd降价文档。我只是尝试在非Markdown R脚本中运行相同的代码，并且运行良好。这个问题肯定与降价有关。

EDIT2：^^从不知道，即使没有.Rmd文件，问题依然存在。将该脚本另存为普通.R脚本后，它将导致rsession再次挂起。编辑3：我忘记提及这是最近发生的事情，可能是由更新的R版本，Rstudio版本或系统库引起的。昨天我能够在Rstudio中没有任何问题的情况下编辑此脚本。本周我更新了Rstudio，但直到几天后才看到这个问题。我很快更新了我的系统，之后很可能还更新了R版本。我只是在努力了解这是如何导致目前的问题。

编辑4：发现了一段代码导致错误，张贴如下。

rsession的回溯时发生错误（编辑后的文件）

Thread 1 "rsession" received signal SIGTERM, Terminated. 
0x00007fbd0cb5ab38 in ??() from /usr/lib/R/lib/libR.so 
(gdb) backtrace 
#0 0x00007fbd0cb5ab38 in ??() from /usr/lib/R/lib/libR.so 
#1 0x00007fbd0cb71196 in ??() from /usr/lib/R/lib/libR.so 
#2 0x00007fbd0cb72499 in ??() from /usr/lib/R/lib/libR.so 
#3 0x00007fbd0cb6ae8c in Rf_eval() from /usr/lib/R/lib/libR.so 
#4 0x00007fbd0cb6b3b9 in ??() from /usr/lib/R/lib/libR.so 
#5 0x00007fbd0cb6b878 in ??() from /usr/lib/R/lib/libR.so 
#6 0x00007fbd0cb6132d in ??() from /usr/lib/R/lib/libR.so 
#7 0x00007fbd0cb6aa88 in Rf_eval() from /usr/lib/R/lib/libR.so 
#8 0x00007fbd0cb6b3b9 in ??() from /usr/lib/R/lib/libR.so 
#9 0x00007fbd0cb6b878 in ??() from /usr/lib/R/lib/libR.so 
#10 0x00007fbd0cb6132d in ??() from /usr/lib/R/lib/libR.so 
#11 0x00007fbd0cb6aa88 in Rf_eval() from /usr/lib/R/lib/libR.so 
#12 0x00007fbd0cb6b3b9 in ??() from /usr/lib/R/lib/libR.so 
#13 0x00007fbd0cb6b878 in ??() from /usr/lib/R/lib/libR.so 
#14 0x00007fbd0cb6132d in ??() from /usr/lib/R/lib/libR.so 
#15 0x00007fbd0cb6aa88 in Rf_eval() from /usr/lib/R/lib/libR.so 
#16 0x00007fbd0cb6b3b9 in ??() from /usr/lib/R/lib/libR.so 
#17 0x00007fbd0cb6b878 in ??() from /usr/lib/R/lib/libR.so 
#18 0x00007fbd0cb6132d in ??() from /usr/lib/R/lib/libR.so 
#19 0x00007fbd0cb6aa88 in Rf_eval() from /usr/lib/R/lib/libR.so 
#20 0x00007fbd0cb6b3b9 in ??() from /usr/lib/R/lib/libR.so 
#21 0x00007fbd0cb6b878 in ??() from /usr/lib/R/lib/libR.so 
#22 0x00007fbd0cb6132d in ??() from /usr/lib/R/lib/libR.so 
#23 0x00007fbd0cb6aa88 in Rf_eval() from /usr/lib/R/lib/libR.so 
#24 0x00007fbd0cb6ceaf in ??() from /usr/lib/R/lib/libR.so 
#25 0x00007fbd0cb623c0 in ??() from /usr/lib/R/lib/libR.so 
#26 0x00007fbd0cb6aa88 in Rf_eval() from /usr/lib/R/lib/libR.so 
#27 0x00007fbd0cb6ceaf in ??() from /usr/lib/R/lib/libR.so 
#28 0x00007fbd0cb623c0 in ??() from /usr/lib/R/lib/libR.so 
#29 0x00007fbd0cb6aa88 in Rf_eval() from /usr/lib/R/lib/libR.so 
#30 0x00007fbd0cb6ceaf in ??() from /usr/lib/R/lib/libR.so 
#31 0x00007fbd0cb623c0 in ??() from /usr/lib/R/lib/libR.so 
#32 0x00007fbd0cb6aa88 in Rf_eval() from /usr/lib/R/lib/libR.so 
#33 0x00007fbd0cb6ceaf in ??() from /usr/lib/R/lib/libR.so 
#34 0x00007fbd0cb623c0 in ??() from /usr/lib/R/lib/libR.so 
#35 0x00007fbd0cb6aa88 in Rf_eval() from /usr/lib/R/lib/libR.so 
#36 0x00007fbd0cb6ceaf in ??() from /usr/lib/R/lib/libR.so 
#37 0x00007fbd0cb6ac56 in Rf_eval() from /usr/lib/R/lib/libR.so 
#38 0x00007fbd0cb1a58e in ??() from /usr/lib/R/lib/libR.so 
---Type <return> to continue, or q <return> to quit--- 
#39 0x00007fbd0cb1bac1 in R_ToplevelExec() from /usr/lib/R/lib/libR.so 
#40 0x00007fbd0cb1bb09 in R_tryEval() from /usr/lib/R/lib/libR.so 
#41 0x0000000000de4189 in rstudio::r::exec::(anonymous namespace)::evaluateExpressionsUnsafe(SEXPREC*, SEXPREC*, SEXPREC**, rstudio::r::sexp::Protect*, rstudio::r::exec::(anonymous namespace)::EvalType) [clone .constprop.57]() 
#42 0x0000000000de5d55 in rstudio::r::exec::evaluateString(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, SEXPREC**, rstudio::r::sexp::Protect*)() 
#43 0x000000000070c85f in rstudio::session::modules::rparser::(anonymous namespace)::resolveObjectAssociatedWithCall(rstudio::core::r_util::token_cursor::RTokenCursor, rstudio::r::sexp::Protect*, bool, bool*) [clone .constprop.1377]() 
#44 0x000000000070e3f7 in rstudio::session::modules::rparser::(anonymous namespace)::mightPerformNonstandardEvaluation(rstudio::core::r_util::token_cursor::RTokenCursor const&, rstudio::session::modules::rparser::ParseStatus&)() 
#45 0x0000000000997dd2 in rstudio::session::modules::rparser::doParse(rstudio::core::r_util::token_cursor::RTokenCursor&, rstudio::session::modules::rparser::ParseStatus&)() 
#46 0x000000000099a320 in rstudio::session::modules::rparser::parse(rstudio::core::FilePath const&, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&, rstudio::session::modules::rparser::ParseOptions const&)() 
#47 0x00000000008a9e65 in rstudio::session::modules::diagnostics::parse(std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&, rstudio::core::FilePath const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)() 
#48 0x00000000008adf66 in rstudio::session::modules::diagnostics::(anonymous namespace)::lintRSourceDocument(rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*)() 
#49 0x0000000000783a0f in rstudio_boost::detail::function::function_invoker2<rstudio::core::Error (*)(rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*), rstudio::core::Error, rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*>::invoke(rstudio_boost::detail::function::function_buffer&, rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*)() 
#50 0x0000000000c5f898 in rstudio::core::json::(anonymous namespace)::runSynchronousFunction(rstudio_boost::function<rstudio::core::Error (rstudio::core::json::JsonRpcRequest const&, rstudio::core::json::JsonRpcResponse*)> const&, rstudio::core::json::JsonRpcRequest const&, rstudio_boost::function<void (rstudio::core::Error const&, rstudio::core::json::JsonRpcResponse*)> const&)() 
#51 0x00000000007e46f9 in rstudio::session::rpc::handleRpcRequest(rstudio::core::json::JsonRpcRequest const&, rstudio_boost::shared_ptr<rstudio::session::HttpConnection>, rstudio::session::http_methods::ConnectionType)() 
#52 0x00000000007e99bb in rstudio::session::http_methods::handleConnection(rstudio_boost::shared_ptr<rstudio::session::HttpConnection>, rstudio::session::http_methods::ConnectionType)() 
#53 0x00000000007ebc8b in rstudio::session::http_methods::waitForMethod(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, rstudio_boost::function<void()> const&, rstudio_boost::function<bool()> const&, rstudio::core::json::JsonRpcRequest*)() 
#54 0x0000000000754b13 in rstudio::session::console_input::rConsoleRead(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, rstudio::r::session::RConsoleInput*)() 
#55 0x0000000000e22cba in rstudio::r::session::RReadConsole(char const*, unsigned char*, int, int)() 
#56 0x00007fbd0cb9431c in Rf_ReplIteration() from /usr/lib/R/lib/libR.so 
---Type <return> to continue, or q <return> to quit--- 
#57 0x00007fbd0cb94811 in ??() from /usr/lib/R/lib/libR.so 
#58 0x00007fbd0cb948c8 in run_Rmainloop() from /usr/lib/R/lib/libR.so 
#59 0x0000000000e4098f in 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*)() 
#60 0x0000000000e1ef3f in rstudio::r::session::run(rstudio::r::session::ROptions const&, rstudio::r::session::RCallbacks const&)() 
#61 0x0000000000718a83 in main()

rstudio诊断：

[1] "1.1.383" 

$R 
[1] "/usr/bin/R" 

$pdflatex 
[1] "/usr/bin/pdflatex" 

$bibtex 
[1] "/usr/bin/bibtex" 

$gcc 
[1] "/usr/bin/gcc" 

$git 
[1] "/usr/bin/git" 

$svn 
[1] "" 

R version 3.4.2 (2017-09-28) 
Platform: x86_64-pc-linux-gnu (64-bit) 
Running under: Ubuntu 16.04.3 LTS 

Matrix products: default 
BLAS: /usr/lib/libblas/libblas.so.3.6.0 
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 

locale: 
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C 
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 

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

loaded via a namespace (and not attached): 
[1] compiler_3.4.2 tools_3.4.2 yaml_2.1.14 

SysInfo: 
sysname release 
"Linux" "4.4.0-97-generic" 
version nodename 
"#120-Ubuntu SMP Tue Sep 19 17:28:18 UTC 2017" "reilly-Precision-7510" 
machine login 
"x86_64" "unknown" 
user effective_user 
"reilly" "reilly" 

R Version: 
_ 
platform x86_64-pc-linux-gnu 
arch x86_64 
os linux-gnu 
system x86_64, linux-gnu 
status 
major 3 
minor 4.2 
year 2017 
month 09 
day 28 
svn rev 73368 
language R 
version.string R version 3.4.2 (2017-09-28) 
nickname Short Summer 
$CLICOLOR_FORCE 
[1] "1" 

$CLUTTER_IM_MODULE 
[1] "xim" 

$COMPIZ_BIN_PATH 
[1] "/usr/bin/" 

$COMPIZ_CONFIG_PROFILE 
[1] "ubuntu" 

$DBUS_SESSION_BUS_ADDRESS 
[1] "unix:abstract=/tmp/dbus-O9bssVywYW" 

$DEFAULTS_PATH 
[1] "/usr/share/gconf/ubuntu.default.path" 

$DERBY_HOME 
[1] "/usr/lib/jvm/java-8-oracle/db" 

$DESKTOP_SESSION 
[1] "ubuntu" 

$DISPLAY 
[1] ":0" 

$EDITOR 
[1] "vi" 

$GDM_LANG 
[1] "en_US" 

$GDMSESSION 
[1] "ubuntu" 

$GIO_LAUNCHED_DESKTOP_FILE 
[1] "/usr/share/applications/rstudio.desktop" 

$GIO_LAUNCHED_DESKTOP_FILE_PID 
[1] "4600" 

$GIT_ASKPASS 
[1] "rpostback-askpass" 

$GNOME_DESKTOP_SESSION_ID 
[1] "this-is-deprecated" 

$GNOME_KEYRING_CONTROL 
[1] "" 

$GNOME_KEYRING_PID 
[1] "" 

$GPG_AGENT_INFO 
[1] "/home/reilly/.gnupg/S.gpg-agent:0:1" 

$GTK2_MODULES 
[1] "overlay-scrollbar" 

$GTK_IM_MODULE 
[1] "ibus" 

$GTK_MODULES 
[1] "gail:atk-bridge:unity-gtk-module" 

$HOME 
[1] "/home/reilly" 

$IM_CONFIG_PHASE 
[1] "1" 

$INSTANCE 
[1] "" 

$J2REDIR 
[1] "/usr/lib/jvm/java-8-oracle/jre" 

$J2SDKDIR 
[1] "/usr/lib/jvm/java-8-oracle" 

$JAVA_HOME 
[1] "/usr/lib/jvm/java-8-oracle" 

$JOB 
[1] "unity-settings-daemon" 

$LANG 
[1] "en_US.UTF-8" 

$LANGUAGE 
[1] "en_US" 

$LD_LIBRARY_PATH 
[1] "/usr/lib/R/lib:/home/bmreilly/software/ncbi/lib64:/home/reilly/software/ncbi/lib64::::/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server:/home/bmreilly/software/ncbi/lib64:/home/reilly/software/ncbi/lib64:" 

$LN_S 
[1] "ln -s" 

$LOGNAME 
[1] "reilly" 

$MAKE 
[1] "make" 

$MANDATORY_PATH 
[1] "/usr/share/gconf/ubuntu.mandatory.path" 

$NGS_LIBDIR 
[1] "/home/bmreilly/software/ncbi/lib64" 

$PAGER 
[1] "/usr/bin/pager" 

$PATH 
[1] "/home/reilly/software/ncbi/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin" 

$PWD 
[1] "/home/reilly" 

$QT4_IM_MODULE 
[1] "xim" 

$QT_ACCESSIBILITY 
[1] "1" 

$QT_IM_MODULE 
[1] "ibus" 

$QT_LINUX_ACCESSIBILITY_ALWAYS_ON 
[1] "1" 

$QT_QPA_PLATFORMTHEME 
[1] "appmenu-qt5" 

$R_BROWSER 
[1] "xdg-open" 

$R_BZIPCMD 
[1] "/bin/bzip2" 

$R_DOC_DIR 
[1] "/usr/share/R/doc" 

$R_GZIPCMD 
[1] "/bin/gzip -n" 

$R_HOME 
[1] "/usr/lib/R" 

$R_INCLUDE_DIR 
[1] "/usr/share/R/include" 

$R_LIBS_SITE 
[1] "/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library" 

$R_LIBS_USER 
[1] "~/R/x86_64-pc-linux-gnu-library/3.4" 

$RMARKDOWN_MATHJAX_PATH 
[1] "/usr/lib/rstudio/resources/mathjax-26" 

$R_PAPERSIZE 
[1] "letter" 

$R_PAPERSIZE_USER 
[1] "letter" 

$R_PDFVIEWER 
[1] "/usr/bin/xdg-open" 

$R_PLATFORM 
[1] "x86_64-pc-linux-gnu" 

$R_PRINTCMD 
[1] "/usr/bin/lpr" 

$R_RD4PDF 
[1] "times,inconsolata,hyper" 

$R_SESSION_TMPDIR 
[1] "/tmp/RtmpYB9etw" 

$R_SHARE_DIR 
[1] "/usr/share/R/share" 

$RS_LOCAL_PEER 
[1] "/tmp/18469-rsession" 

$RS_PPM_FD_READ 
[1] "21" 

$RS_PPM_FD_WRITE 
[1] "22" 

$RS_RPOSTBACK_PATH 
[1] "/usr/lib/rstudio/bin/rpostback" 

$RS_SHARED_SECRET 
[1] "16816927778469308861804289383" 

$RSTUDIO 
[1] "1" 

$RSTUDIO_CONSOLE_COLOR 
[1] "256" 

$RSTUDIO_CONSOLE_WIDTH 
[1] "109" 

$RSTUDIO_PANDOC 
[1] "/usr/lib/rstudio/bin/pandoc" 

$RSTUDIO_SESSION_PORT 
[1] "18469" 

$RSTUDIO_USER_IDENTITY 
[1] "reilly" 

$RSTUDIO_WINUTILS 
[1] "bin/winutils" 

$R_SYSTEM_ABI 
[1] "linux,gcc,gxx,gfortran,?" 

$R_TEXI2DVICMD 
[1] "/usr/bin/texi2dvi" 

$R_UNZIPCMD 
[1] "/usr/bin/unzip" 

$R_ZIPCMD 
[1] "/usr/bin/zip" 

$SED 
[1] "/bin/sed" 

$SESSION 
[1] "ubuntu" 

$SESSIONTYPE 
[1] "gnome-session" 

$SHELL 
[1] "/bin/bash" 

$SHLVL 
[1] "0" 

$SSH_AUTH_SOCK 
[1] "/run/user/1000/keyring/ssh" 

$TAR 
[1] "/bin/tar" 

$TERM 
[1] "xterm-256color" 

$UPSTART_EVENTS 
[1] "xsession started" 

$UPSTART_INSTANCE 
[1] "" 

$UPSTART_JOB 
[1] "unity7" 

$UPSTART_SESSION 
[1] "unix:abstract=/com/ubuntu/upstart-session/1000/1585" 

$USER 
[1] "reilly" 

$XAUTHORITY 
[1] "/home/reilly/.Xauthority" 

$XDG_CONFIG_DIRS 
[1] "/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg" 

$XDG_CURRENT_DESKTOP 
[1] "Unity" 

$XDG_DATA_DIRS 
[1] "/usr/share/ubuntu:/usr/share/gnome:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop" 

$XDG_GREETER_DATA_DIR 
[1] "/var/lib/lightdm-data/reilly" 

$XDG_MENU_PREFIX 
[1] "gnome-" 

$XDG_RUNTIME_DIR 
[1] "/run/user/1000" 

$XDG_SEAT 
[1] "seat0" 

$XDG_SEAT_PATH 
[1] "/org/freedesktop/DisplayManager/Seat0" 

$XDG_SESSION_DESKTOP 
[1] "ubuntu" 

$XDG_SESSION_ID 
[1] "c2" 

$XDG_SESSION_PATH 
[1] "/org/freedesktop/DisplayManager/Session0" 

$XDG_SESSION_TYPE 
[1] "x11" 

$XDG_VTNR 
[1] "7" 

$XMODIFIERS 
[1] "@im=ibus" 

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

(Empty) 

Log file: rsession-reilly.log 
-------------------------------------------------- 

13 Oct 2017 21:15:06 [rsession-reilly] WARNING Process supervisor did not terminate within 1 second; LOGGED FROM: void {anonymous}::rCleanup(bool) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:1099

这是导致错误的代码段。

当这段代码保存到文档中时，在打开和编辑文件时，rsession挂起。如果这段代码不存在，文档工作正常。不完全确定发生了什么事。这段代码只是我正在研究的一个未完成的功能，但不知何故它正在炸毁Rstudio。

iteratively_impute_pca_zscore_remove_outliers <- function(matrix, ...) { 
    repeat { 
    imputed.mat <- impute_less_than_x_NA(matrix) 
    pc1_score_ 
    if (length(SamplesToRemove)==0) 
    } 
} 
repeat { 

} (length(samplesToRemove)==0){ 

}

来源

2017-10-13 Reilstein

从回溯中看来，RStudio诊断引擎可能会卡住文件中的某些内容。你有没有机会分享你正在编辑的文档并保存？或者它是否会出现在任何类型的R文档中？ –

你是对的！似乎这个问题出现在一些具体的文件中。我认为这可能是因为R文件在Rstudio中未打开时打开文件而导致R崩溃或与服务器的连接崩溃。现在每当我尝试编辑这些文档时，它都会崩溃。我无法分享文档，因为它们是非常大的knitr文档。你对我如何恢复这些损坏的文件中的信息有什么想法吗？即将一个简单的复制/粘贴到新的文档工作？ – Reilstein

您可以尝试使用其他编辑器（RStudio以外的其他编辑器）打开它们，然后将内容复制并粘贴到一个[GitHub Gist]（https://gist.github.com/），并共享链接。也许值得尝试[重置RStudio的状态]（https://support.rstudio.com/hc/en-us/articles/200534577-Resetting-RStudio-Desktop-s-State）。 –

Oof！感谢您报告并通过评论讨论此问题。这里的问题是这段代码：（！）

repeat { 

} (length(samplesToRemove)==0){ 

}

的问题是，要RStudio的诊断系统，这看起来像一个函数调用，其中repeat {}是函数的左侧被调用。当RStudio尝试评估此功能时，它会卡在repeat {}循环中，并且永远不会有机会逃脱。

您应该能够通过移动该位为一个独立的行来解决此问题：

repeat { 

} 

(length(samplesToRemove)==0){ 

}

但我会提交本作的RStudio人，我们会尽力得到修复。

来源

2017-10-15 06:40:09

感谢您对诊断问题的帮助，并提出问题！这是一个令人头痛的问题，我只是在我的绳索末端。我真的不认为这是打破Rstudio的代码本身。现在我更了解了Rstudio在幕后做了些什么，我将来会注意到这一点！ – Reilstein

我很高兴我能够帮助！感谢您坚持不懈地解决这个问题;我相信遇到并处理这件事令人沮丧。 –

Rstudio rsession在编辑文件时挂起

rsession的回溯时发生错误（编辑后的文件）

rstudio诊断：

这是导致错误的代码段。

回答

相关问题