After starting Rstudio the icon only "blinks" but nothing happens

mmatt · May 30, 2018, 4:38pm

I am having the same problem on Ubuntu 16.04 LTS using R 3.4.4 and RStudio rstudio-xenial-1.1.453-amd64 that after starting Rstudio the icon only "blinks" but nothing happens/ no window is popping up.

Also found a similar open comment on Github
RStudio is blank upon start, It is broken. #2885

github.com/rstudio/rstudio

RStudio is blank upon start, It is broken.

opened 11:45AM - 30 May 18 UTC

closed 04:08AM - 06 Jun 18 UTC

irshad001

info needed

### System details RStudio Edition : RStudio Version : rstudio-xenial-1.1.453-amd64 OS Version : Ubuntu 16.04 LTS R Version : R version 3.4.4 (2018-03-15) ### Describe the problem in detail RStudio was working fine in the morning. However, it has suddenly hung. And when I try to kill the process and reopened it. But it did not open. It is completely blank. I can see other windows in the transparent screen of Rstudio. My R is working fine. It never occured to me before. I uninstalled and re-installed both R and Rstudio as well but problem still persists. I have ran the diagnostics on my system, it produced a file and and output. Using R script: /usr/bin/R Attempting to launch R session... R_HOME=/usr/lib/R R_DOC_DIR=/usr/share/R/doc R_INCLUDE_DIR=/usr/share/R/include R_SHARE_DIR=/usr/share/R/share LD_LIBRARY_PATH=/usr/lib/R/lib:/usr/local/oracle/instantclient_11_2/::::/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server:/usr/local/oracle/instantclient_11_2/: PATH=/home/irshad/bin:/home/irshad/.local/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 HOME=/home/irshad R session launched, attempting to connect on port 29984... Connected to R session, attempting to initialize... Successfully initialized R session. Diagnostics report written to: /home/irshad/rstudio-diagnostics/diagnostics-report.txt (nautilus:8246): GLib-GIO-CRITICAL **: g_dbus_interface_skeleton_unexport: assertion 'interface_->priv->connections != NULL' failed (nautilus:8246): GLib-GIO-CRITICAL **: g_dbus_interface_skeleton_unexport: assertion 'interface_->priv->connections != NULL' failed (nautilus:8246): Gtk-CRITICAL **: gtk_icon_theme_get_for_screen: assertion 'GDK_IS_SCREEN (screen)' failed (nautilus:8246): GLib-GObject-WARNING **: invalid (NULL) pointer instance (nautilus:8246): GLib-GObject-CRITICAL **: g_signal_connect_object: assertion 'G_TYPE_CHECK_INSTANCE (instance)' failed QApplication::qAppName: Please instantiate the QApplication object first file I am attaching here: [diagnostics-report.txt](https://github.com/rstudio/rstudio/files/2053714/diagnostics-report.txt)

I have been using keras for R with tensorflow backend and the same also in Python. Sometimes RStudio failed to start if I used a python notebook with keras TF right before. But a reboot usually solved the problem.

Today I have tried most of the trouble shooting steps.

deleted RData, history etc. files
deleting .rstudio-desktop
removing and reinstallling Rstudio (R 3.4.4 and RStudio 1.1.453)
removing R and Rstudio => reinstalling R. 3.4.3 and RStudio (rstudio-1.0.153-amd64.deb), currently this combination of versions is on my computer

Running rstudio from the terminal gives the following error:

load glyph failed err=6 face=0x108fed0, glyph=2797
load glyph failed err=6 face=0x108fed0, glyph=2797
"Invalid splitter position detected: 11/0"
"Invalid splitter position detected: 16/0"
"Invalid splitter position detected: 11/0"
"Invalid splitter position detected: 16/0"
"Invalid splitter position detected: 11/0"
"Invalid splitter position detected: 16/0"

Running diagnostics rstudio --run-diagnostics gives this output:

Using R script: /usr/bin/R

Attempting to launch R session...
  R_HOME=/usr/lib/R
  R_DOC_DIR=/usr/share/R/doc
  R_INCLUDE_DIR=/usr/share/R/include
  R_SHARE_DIR=/usr/share/R/share
  LD_LIBRARY_PATH=/usr/lib/R/lib::/usr/local/cuda/lib64:::/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/jre/lib/amd64/server::/usr/local/cuda/lib64
  PATH=/usr/local/cuda/bin:/home/matt/bin:/home/matt/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
  HOME=/home/matt

R session launched, attempting to connect on port 14937...

Connected to R session, attempting to initialize...

Successfully initialized R session.

Diagnostics report written to: /home/matt/rstudio-diagnostics/diagnostics-report.txt

(nautilus:5155): GLib-GIO-CRITICAL **: g_dbus_interface_skeleton_unexport: assertion 'interface_->priv->connections != NULL' failed

(nautilus:5155): GLib-GIO-CRITICAL **: g_dbus_interface_skeleton_unexport: assertion 'interface_->priv->connections != NULL' failed

(nautilus:5155): Gtk-CRITICAL **: gtk_icon_theme_get_for_screen: assertion 'GDK_IS_SCREEN (screen)' failed

(nautilus:5155): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(nautilus:5155): GLib-GObject-CRITICAL **: g_signal_connect_object: assertion 'G_TYPE_CHECK_INSTANCE (instance)' failed
QApplication::qAppName: Please instantiate the QApplication object first

I would really appreciate some help. Cause reinstallilng my whole system is not an option.

Thank You.

kevinushey · May 31, 2018, 9:04pm

It would be useful to see the contents of the generated diagnostics report.

mmatt · June 1, 2018, 5:19pm

Dear Kevin,

thank you for your reply. Below is the text from the diagnostics-report.txt

[1] "1.0.153"

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

$pdflatex
[1] ""

$bibtex
[1] ""

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

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

$svn
[1] ""

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.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_3.4.3 tools_3.4.3   

SysInfo:
                                              sysname 
                                              "Linux" 
                                              release 
                                  "4.13.0-43-generic" 
                                              version 
"#48~16.04.1-Ubuntu SMP Thu May 17 12:56:46 UTC 2018" 
                                             nodename 
                                             "zephyr" 
                                              machine 
                                             "x86_64" 
                                                login 
                                            "unknown" 
                                                 user 
                                               "matt" 
                                       effective_user 
                                               "matt" 

R Version:
               _                           
platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          4.3                         
year           2017                        
month          11                          
day            30                          
svn rev        73796                       
language       R                           
version.string R version 3.4.3 (2017-11-30)
nickname       Kite-Eating Tree            
$`_`
[1] "/usr/bin/rstudio"

$CLUTTER_IM_MODULE
[1] "xim"

$COMPIZ_CONFIG_PROFILE
[1] "ubuntu"

$CUDA_HOME
[1] "/usr/local/cuda"

$DBUS_SESSION_BUS_ADDRESS
[1] "unix:abstract=/tmp/dbus-QWS1cF4RFx"

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

$DESKTOP_SESSION
[1] "ubuntu"

$DISPLAY
[1] ":0"

$EDITOR
[1] "vi"

$GDM_LANG
[1] "en_US"

$GDMSESSION
[1] "ubuntu"

$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/matt/.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/matt"

$IM_CONFIG_PHASE
[1] "1"

$INSTANCE
[1] "Unity"

$JOB
[1] "gnome-session"

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

$LANGUAGE
[1] "en_US"

$LC_ADDRESS
[1] "de_DE.UTF-8"

$LC_IDENTIFICATION
[1] "de_DE.UTF-8"

$LC_MEASUREMENT
[1] "de_DE.UTF-8"

$LC_MONETARY
[1] "de_DE.UTF-8"

$LC_NAME
[1] "de_DE.UTF-8"

$LC_NUMERIC
[1] "de_DE.UTF-8"

$LC_PAPER
[1] "de_DE.UTF-8"

$LC_TELEPHONE
[1] "de_DE.UTF-8"

$LC_TIME
[1] "de_DE.UTF-8"

$LD_LIBRARY_PATH
[1] "/usr/lib/R/lib::/usr/local/cuda/lib64:::/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/jre/lib/amd64/server::/usr/local/cuda/lib64"

$LESSCLOSE
[1] "/usr/bin/lesspipe %s %s"

$LESSOPEN
[1] "| /usr/bin/lesspipe %s"

$LN_S
[1] "ln -s"

$LOGNAME
[1] "matt"

$LS_COLORS
[1] "rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:"

$MAKE
[1] "make"

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

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

$PATH
[1] "/usr/local/cuda/bin:/home/matt/bin:/home/matt/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"

$PWD
[1] "/home/matt"

$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] "a4"

$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/RtmpKZ5ZGl"

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

$RS_LOCAL_PEER
[1] "/tmp/14937-rsession"

$RS_PPM_FD_READ
[1] "20"

$RS_PPM_FD_WRITE
[1] "21"

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

$RS_SHARED_SECRET
[1] "16816927778469308861804289383"

$RSTUDIO
[1] "1"

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

$RSTUDIO_SESSION_PORT
[1] "14937"

$RSTUDIO_USER_IDENTITY
[1] "matt"

$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"

$SESSIONTYPE
[1] "gnome-session"

$SHELL
[1] "/bin/bash"

$SHLVL
[1] "1"

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

$TAR
[1] "/bin/tar"

$TERM
[1] "xterm-256color"

$UPSTART_EVENTS
[1] "started starting"

$UPSTART_INSTANCE
[1] ""

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

$UPSTART_SESSION
[1] "unix:abstract=/com/ubuntu/upstart-session/1000/1278"

$USER
[1] "matt"

$VTE_VERSION
[1] "4205"

$WINDOWID
[1] "71303290"

$XAUTHORITY
[1] "/home/matt/.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:/var/lib/snapd/desktop"

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

$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"    
 [4] "package:graphics"  "package:grDevices" "package:utils"    
 [7] "package:datasets"  "package:methods"   "Autoloads"        
[10] "package:base"     
Log file: rdesktop.log
--------------------------------------------------

(Empty)

Log file: rsession-matt.log
--------------------------------------------------

(Not Found)

kevinushey · June 1, 2018, 6:50pm

You said you installed RStudio v1.1.453, but the version of RStudio being launched in the diagnostics report is reporting itself as version 1.0.153. Is it possible something went wrong during the attempt to upgrade to RStudio v1.1?

You might try purging your RStudio installation and then attempting to reinstall once more.

mmatt · June 1, 2018, 8:29pm

No. Neither versions worked sadly. I did not attempt an upgrade.

This error suddenly occured on the next day after I have installed R and Python packages using R 3.4.4 and RStudio rstudio-xenial-1.1.453-amd64.

During troubleshooting I have reinstalled both R and RStudio. Because of the post here and on GitHub I have also decided to downgrade but that did not help either.

"[...] Reinstalling R. 3.4.3 and RStudio (rstudio-1.0.153-amd64.deb), currently this combination of versions is on my computer. [...]"

Thank you Kevin that you are looking into this problem.

system · September 11, 2019, 8:12pm

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