Unexpected RStudio (version 1.1.463) crashes on arch linux


#1

I'm experiencing frequent and unexpected crashes of RStudio on Arch Linux. I'm running version 1.1.463 and it was installed via converted .deb package. There doesn't seem to be any specific action that crashes it, it crashed during a package install, during the execution of the cv.glmnet function from the glmnet package and even when it was idling.

I've also generated a diagnostics-report, its contents:

[1] "1.1.463"

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

$pdflatex
[1] ""

$bibtex
[1] ""

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

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

$svn
[1] ""

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Matrix products: default
BLAS: /usr/lib/libopenblasp-r0.3.3.so
LAPACK: /usr/lib/liblapack.so.3.8.0

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
[7] base

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

SysInfo:
sysname
"Linux"
release
"4.19.4-arch1-1-ARCH"
version
"#1 SMP PREEMPT Fri Nov 23 09:06:58 UTC 2018"
nodename
"numbercrunsher"
machine
"x86_64"
login
"qubit"
user
"qubit"
effective_user
"qubit"

R Version:
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
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
$CLICOLOR_FORCE
[1] "1"

$DBUS_SESSION_BUS_ADDRESS
[1] "unix:path=/run/user/1000/bus"

$DESKTOP_SESSION
[1] "/usr/share/xsessions/plasma"

$DISPLAY
[1] ":0"

$EDITOR
[1] "vi"

$GIT_ASKPASS
[1] "rpostback-askpass"

$GS_LIB
[1] "/home/qubit/.fonts"

$GTK_MODULES
[1] "canberra-gtk-module"

$HOME
[1] "/home/qubit"

$KDE_FULL_SESSION
[1] "true"

$KDE_SESSION_UID
[1] "1000"

$KDE_SESSION_VERSION
[1] "5"

$KDEDIRS
[1] "/usr"

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

$LD_LIBRARY_PATH
[1] "/usr/lib64/R/lib::/lib:/usr/lib/jvm/java-7-openjdk/jre/lib/amd64/server"

$LN_S
[1] "ln -s"

$LOGNAME
[1] "qubit"

$MAIL
[1] "/var/spool/mail/qubit"

$MAKE
[1] "make"

$MOZ_PLUGIN_PATH
[1] "/usr/lib/mozilla/plugins"

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

$PAM_KWALLET5_LOGIN
[1] "/run/user/1000/kwallet5.socket"

$PATH
[1] "/usr/local/sbin:/usr/local/bin:/usr/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl"

$PWD
[1] "/home/qubit"

$QT_AUTO_SCREEN_SCALE_FACTOR
[1] "0"

$QT_DIR
[1] "/usr/lib/rstudio/bin"

$QT_IM_MODULE
[1] "compose"

$QT_PLUGIN_PATH
[1] "/usr/lib/rstudio/bin/plugins"

$QT_QPA_PLATFORM_PLUGIN_PATH
[1] "/usr/lib/rstudio/bin/plugins/platforms"

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

$R_BZIPCMD
[1] "/usr/bin/bzip2"

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

$R_GZIPCMD
[1] "/usr/bin/gzip"

$R_HOME
[1] "/usr/lib64/R"

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

$R_LIBS_SITE
[1] ""

$R_LIBS_USER
[1] "~/R/x86_64-pc-linux-gnu-library/3.5"

$R_PAPERSIZE
[1] "a4"

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

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

$R_PRINTCMD
[1] ""

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

$R_SESSION_TMPDIR
[1] "/tmp/Rtmp4oyoIr"

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

$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"

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

$RS_LOCAL_PEER
[1] "/tmp/31375-rsession"

$RS_PPM_FD_READ
[1] "11"

$RS_PPM_FD_WRITE
[1] "12"

$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] "63"

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

$RSTUDIO_SESSION_PORT
[1] "31375"

$RSTUDIO_USER_IDENTITY
[1] "qubit"

$RSTUDIO_WINUTILS
[1] "bin/winutils"

$SED
[1] "/usr/bin/sed"

$SESSION_MANAGER
[1] "local/numbercrunsher:@/tmp/.ICE-unix/9255,unix/numbercrunsher:/tmp/.ICE-unix/9255"

$SHELL
[1] "/bin/bash"

$SHLVL
[1] "1"

$TAR
[1] "/usr/bin/tar"

$TERM
[1] "xterm-256color"

$USER
[1] "qubit"

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

$XCURSOR_THEME
[1] "breeze_cursors"

$XDG_CURRENT_DESKTOP
[1] "KDE"

$XDG_DATA_DIRS
[1] "/usr/share:/usr/share:/usr/local/share"

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

$XDG_SEAT
[1] "seat0"

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

$XDG_SESSION_CLASS
[1] "user"

$XDG_SESSION_DESKTOP
[1] "KDE"

$XDG_SESSION_ID
[1] "5"

$XDG_SESSION_PATH
[1] "/org/freedesktop/DisplayManager/Session3"

$XDG_SESSION_TYPE
[1] "x11"

$XDG_VTNR
[1] "1"

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

(Empty)

Log file: rsession-qubit.log

06 Dec 2018 03:17:08 [rsession-qubit] CLIENT EXCEPTION (rsession-qubit): (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 (X11 Linux x86_64) AppleWebKit/538.1 (KHTML, like Gecko) RStudio Safari/538.1 Qt/5.4.0
06 Dec 2018 03:17:08 [rsession-qubit] CLIENT EXCEPTION (rsession-qubit): (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 (X11 Linux x86_64) AppleWebKit/538.1 (KHTML, like Gecko) RStudio Safari/538.1 Qt/5.4.0
06 Dec 2018 03:17:08 [rsession-qubit] CLIENT EXCEPTION (rsession-qubit): (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 (X11 Linux x86_64) AppleWebKit/538.1 (KHTML, like Gecko) RStudio Safari/538.1 Qt/5.4.0
06 Dec 2018 03:17:08 [rsession-qubit] CLIENT EXCEPTION (rsession-qubit): (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 (X11 Linux x86_64) AppleWebKit/538.1 (KHTML, like Gecko) RStudio Safari/538.1 Qt/5.4.0
06 Dec 2018 03:56:35 [rsession-qubit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:1239
06 Dec 2018 05:07:58 [rsession-qubit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:1239
06 Dec 2018 08:11:14 [rsession-qubit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:1239

Apart from that I've also collected a core dump from one of the crashes:

Dec 06 09:11:15 numbercrunsher systemd-coredump[25338]: Process 21124 (rsession) of user 1000 dumped core.
#2 0x0000000000df8189 _ZN7rstudio4core6system5abortEv (rsession)
#3 0x00000000007d951b _ZN12_GLOBAL__N_123detectParentTerminationEv (rsession)
#4 0x0000000000c7ec9e _ZN13rstudio_boost6detail11thread_dataINS_8functionIFvvEEEE3runEv (rsession)
#5 0x0000000000f51379 thread_proxy (rsession)
#1 0x0000000000847738 _ZN7rstudio7session19HttpConnectionQueue17waitForConnectionERKN13rstudio_boost10posix_time13time_durationE (rsession)
#2 0x0000000000847e73 _ZN7rstudio7session19HttpConnectionQueue15dequeConnectionERKN13rstudio_boost10posix_time13time_durationE (rsession)
#3 0x000000000072fa73 _ZN7rstudio7session18ClientEventService3runEv (rsession)
#4 0x0000000000f51379 thread_proxy (rsession)
#1 0x0000000000dc5ed0 _ZN7rstudio4core6thread15ThreadsafeQueueINS0_6system12file_monitor12_GLOBAL__N_119RegistrationCommandEE4waitERKN13rstudio_boost10posix_time13time_durationE.isra.450.constprop.738 (rsession)
#2 0x0000000000dc6c62 _ZN7rstudio4core6system12file_monitor12_GLOBAL__N_113checkForInputEv (rsession)
#3 0x0000000000e1ae01 _ZN7rstudio4core6system12file_monitor6detail3runERKN13rstudio_boost8functionIFvvEEE (rsession)
#4 0x0000000000dc63db _ZN7rstudio4core6system12file_monitor12_GLOBAL__N_121fileMonitorThreadMainEv (rsession)
#5 0x0000000000c7ec9e _ZN13rstudio_boost6detail11thread_dataINS_8functionIFvvEEEE3runEv (rsession)
#6 0x0000000000f51379 thread_proxy (rsession)
#57 0x0000000000ec72f2 _ZN7rstudio1r7session12runEmbeddedRERKNS_4core8FilePathES5_bb7SA_TYPERKNS1_9CallbacksEPNS1_17InternalCallbacksE (rsession)
#58 0x0000000000ea682d _ZN7rstudio1r7session3runERKNS1_8ROptionsERKNS1_10RCallbacksE (rsession)
#59 0x000000000070645f main (rsession)
#61 0x00000000007173f5 _start (rsession)

Does anybody know what might be causing these crashes?


#2

Do you have any better luck with the preview release?


#3

I haven't tried it yet, but I will definitely do so. Thanks for the tip!


#4

I have tried the preview version now and haven't encountered any crashes so far. It's still too soon to say that the problem won't occur again, but it is looking a lot better than with version 1.1.463.