Rstudio crashes every ~20 clicks in menus after fresh install Ubuntu 18.04 first time linux user here

vurnhat · November 24, 2019, 9:40pm

While following an installation guide (first time linux user), I apt-get installed r-base, then I installed Rstudio using the deb file from their website, I added a key for I think package updates by submitting this command in terminal:
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

And since installing Rstudio it crashes after a few seconds of clicking around in the menus and doing nothing since fresh install. I have reset the state of my Rstudio Desktop with "mv ~/.rstudio-desktop ~/backup-rstudio-desktop" and even confirmed the file was gone and got replaced upon Rstudio restart. I have no idea how to fix this because it's happening upon a fresh install. Is there some sort of log file I can post to see what is causing the crash? Thanks.

Here is my session Info:

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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 base

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1

vurnhat · November 24, 2019, 9:52pm

Here is the diagnostic report i've seen asked for on other posts:

[1] "1.2.5019"

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

$pdflatex
[1] ""

$bibtex
[1] ""

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

$git
[1] ""

$svn
[1] ""

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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 base

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1

SysInfo:
sysname
"Linux"
release
"5.0.0-36-generic"
version
"#39~18.04.1-Ubuntu SMP Tue Nov 12 11:09:50 UTC 2019"
nodename
"vurnhat-desktop"
machine
"x86_64"
login
"vurnhat"
user
"vurnhat"
effective_user
"vurnhat"

R Version:
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 6.1
year 2019
month 07
day 05
svn rev 76782
language R
version.string R version 3.6.1 (2019-07-05)
nickname Action of the Toes
$_R_CHECK_COMPILATION_FLAGS_KNOWN_
[1] "-Wformat -Werror=format-security -Wdate-time"

$CLICOLOR_FORCE
[1] "1"

$CLUTTER_IM_MODULE
[1] "xim"

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

$DESKTOP_SESSION
[1] "ubuntu"

$DISPLAY
[1] ":0"

$EDITOR
[1] "vi"

$GDMSESSION
[1] "ubuntu"

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

$GIO_LAUNCHED_DESKTOP_FILE_PID
[1] "2745"

$GIT_ASKPASS
[1] "rpostback-askpass"

$GJS_DEBUG_OUTPUT
[1] "stderr"

$GJS_DEBUG_TOPICS
[1] "JS ERROR;JS LOG"

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

$GNOME_SHELL_SESSION_MODE
[1] "ubuntu"

$GPG_AGENT_INFO
[1] "/run/user/1000/gnupg/S.gpg-agent:0:1"

$GTK_IM_MODULE
[1] "ibus"

$GTK_MODULES
[1] "gail:atk-bridge"

$HOME
[1] "/home/vurnhat"

$IM_CONFIG_PHASE
[1] "2"

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

$LD_LIBRARY_PATH
[1] "/usr/lib/R/lib::/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/lib/server"

$LN_S
[1] "ln -s"

$LOGNAME
[1] "vurnhat"

$MAKE
[1] "make"

$MPLENGINE
[1] "tkAgg"

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

$PATH
[1] "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"

$PWD
[1] "/home/vurnhat"

$QT_ACCESSIBILITY
[1] "1"

$QT_IM_MODULE
[1] "xim"

$QT4_IM_MODULE
[1] "xim"

$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/3.6"

$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/Rtmpewx6yS"

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

$R_STRIP_SHARED_LIB
[1] "strip --strip-unneeded"

$R_STRIP_STATIC_LIB
[1] "strip --strip-debug"

$R_SYSTEM_ABI
[1] "linux,gcc,gxx,gfortran,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_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] "74"

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

$RSTUDIO_SESSION_PORT
[1] "46484"

$RSTUDIO_USER_IDENTITY
[1] "vurnhat"

$RSTUDIO_WINUTILS
[1] "bin/winutils"

$SED
[1] "/bin/sed"

$SESSION_MANAGER
[1] "local/vurnhat-desktop:@/tmp/.ICE-unix/1524,unix/vurnhat-desktop:/tmp/.ICE-unix/1524"

$SHELL
[1] "/bin/bash"

$SHLVL
[1] "0"

$SSH_AGENT_PID
[1] "1621"

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

$TAR
[1] "/bin/tar"

$TERM
[1] "xterm-256color"

$TEXTDOMAIN
[1] "im-config"

$TEXTDOMAINDIR
[1] "/usr/share/locale/"

$USER
[1] "vurnhat"

$USERNAME
[1] "vurnhat"

$WINDOWPATH
[1] "2"

$XAUTHORITY
[1] "/run/user/1000/gdm/Xauthority"

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

$XDG_CURRENT_DESKTOP
[1] "ubuntu:GNOME"

$XDG_DATA_DIRS
[1] "/usr/share/ubuntu:/home/vurnhat/.local/share/flatpak/exports/share/:/var/lib/flatpak/exports/share/:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop"

$XDG_MENU_PREFIX
[1] "gnome-"

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

$XDG_SEAT
[1] "seat0"

$XDG_SESSION_DESKTOP
[1] "ubuntu"

$XDG_SESSION_ID
[1] "2"

$XDG_SESSION_TYPE
[1] "x11"

$XDG_VTNR
[1] "2"

$XMODIFIERS
[1] "@im=ibus"

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

(Empty)

Log file: rsession-vurnhat.log

24 Nov 2019 21:26:51 [rsession-vurnhat] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /var/lib/jenkins/workspace/IDE/open-source-pipeline/v1.2-patch/src/cpp/session/SessionMain.cpp:1333
24 Nov 2019 21:27:42 [rsession-vurnhat] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /var/lib/jenkins/workspace/IDE/open-source-pipeline/v1.2-patch/src/cpp/session/SessionMain.cpp:1333
24 Nov 2019 21:34:52 [rsession-vurnhat] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /var/lib/jenkins/workspace/IDE/open-source-pipeline/v1.2-patch/src/cpp/session/SessionMain.cpp:1333
24 Nov 2019 21:45:04 [rsession-vurnhat] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /var/lib/jenkins/workspace/IDE/open-source-pipeline/v1.2-patch/src/cpp/session/SessionMain.cpp:1333
24 Nov 2019 21:45:07 [rsession-vurnhat] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /var/lib/jenkins/workspace/IDE/open-source-pipeline/v1.2-patch/src/cpp/session/SessionMain.cpp:1333
24 Nov 2019 21:50:05 [rsession-vurnhat] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /var/lib/jenkins/workspace/IDE/open-source-pipeline/v1.2-patch/src/cpp/session/SessionMain.cpp:1333

technocrat · November 24, 2019, 10:07pm

Gotta say that for a Linux newcomer, you're coming up to speed fast.

There's a log file under ~/.rstudio-desktop/log/ which may be of help in following the troubleshooting guide. But I kinda doubt it will be much help--it's more for usage errors.

I haven't had to use it myself, but a backtrace will probably be more helpful.

Under the heading of mere suspicions, I smell a permissions issue somewhere--RStudio may be trying to write somewhere and can't.

vurnhat · November 24, 2019, 10:33pm

New users are unable to make posts with more than 2 links, so here is a github repo with the backtrace i just created. Thank you so much for the help!

github.com

vurnhat/rstudio-troubleshooting/blob/master/rstudio_backtrace

RStudio Version: 1.2.5019

> print(sessionInfo())
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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:

This file has been truncated. show original

technocrat · November 24, 2019, 11:34pm

Great. Using github for this kind of info is always great.

Before embarking, I'll note a couple of differences in our environments.

I'm on Pop!_OS 19.10, basically Ubuntu with party attire
I'm at RStudio 1.2.1578
My BLAS and LAPACK are 3.8.0

I don't know if those differences are relevant, but let's just keep them in the back of our minds.

The problem shows up at once:

Program terminated with signal SIGABRT, Aborted.

which was triggered by

/usr/lib/rstudio/bin/rsession --config-file none --program-mode desktop --www-p

A search for that led to a possible configuration issue

Try keeping RStudio alive long enough to change to software rendering and report back?

vurnhat · November 25, 2019, 1:51am

Seems to have worked. Should I make an effort to correct something with my system in order to allow for GPU rendering? My Ubuntu is so fresh, I haven't even downloaded any GPU drivers yet. Once I do that, it could likely fix my issue with using GPU rending on RStudio?

Thank you!

technocrat · November 25, 2019, 2:04am

Great! Please mark that as a solution for the seekers to follow.

I have to confess total ignorance of GPU drivers. I got System 76 specifically so I wouldn't have to worry about going that granular. A fresh install is probably the best time to try, however, before there's too much to restore.

system · December 2, 2019, 2:04am

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.

Rstudio crashes every ~20 clicks in menus after fresh install Ubuntu 18.04 first time linux user here

[1] ".GlobalEnv" "tools:rstudio" "package:stats" [4] "package:graphics" "package:grDevices" "package:utils" [7] "package:datasets" "package:methods" "Autoloads" [10] "package:base" Log file: rdesktop.log

Log file: rsession-vurnhat.log

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