R studio starts with a blank white screen

rstudio

#1

I am using R version 3.4.4 on Ubuntu 17.10, even though R works I am unable to start RStudio.

Diagnostics report

12 Apr 2018 16:38:58 [rdesktop] ERROR R did not return any output when queried for directory location information; LOGGED FROM: bool rstudio::core::r_util::{anonymous}::detectRLocationsUsingR(const string&, rstudio::core::FilePath*, rstudio::core::FilePath*, rstudio::core::config_utils::Variables*, std::__cxx11::string*) /home/ubuntu/rstudio/src/cpp/core/r_util/REnvironmentPosix.cpp:483
12 Apr 2018 16:38:59 [rdesktop] ERROR system error 71 (Protocol error) [description=Unable to parse version from R, version-info=, r-error=Fatal error: unable to open the base package

]; OCCURRED AT: rstudio::core::Error rstudio::core::r_util::rVersion(const rstudio::core::FilePath&, const rstudio::core::FilePath&, const string&, std::__cxx11::string*) /home/ubuntu/rstudio/src/cpp/core/r_util/REnvironmentPosix.cpp:784; LOGGED FROM: bool rstudio::core::r_util::detectREnvironment(const rstudio::core::FilePath&, const rstudio::core::FilePath&, const string&, std::__cxx11::string*, std::__cxx11::string*, rstudio::core::r_util::EnvironmentVars*, std::__cxx11::string*) /home/ubuntu/rstudio/src/cpp/core/r_util/REnvironmentPosix.cpp:678

Using R script: /home/kishore/software/R/R-3.4.3/bin/R

Attempting to launch R session...
RSTUDIO_WHICH_R=/home/kishore/software/R/R-3.4.3/bin/R
R_HOME=/home/kishore/software/R/R-3.4.3/lib/R
R_DOC_DIR=/home/kishore/software/R/R-3.4.3/lib/R/doc
R_INCLUDE_DIR=/home/kishore/software/R/R-3.4.3/lib/R/include
R_SHARE_DIR=/home/kishore/software/R/R-3.4.3/lib/R/share
LD_LIBRARY_PATH=/home/kishore/software/R/R-3.4.3/lib/R/lib::/lib:/usr/local/lib:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server
PATH=PATH=/usr/local/src/R:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/kishore/Documents/tools/geckodriver-v0.19.0-linux64/
HOME=/home/kishore

R session launched, attempting to connect on port 20169...
12 Apr 2018 16:38:59 [rsession-kishore] ERROR R SUICIDE: unable to open the base package
; LOGGED FROM: void {anonymous}::rSuicide(const string&) /home/ubuntu/rstudio/src/cpp/session/SessionMain.cpp:1023

Connected to R session, attempting to initialize...

QApplication::qAppName: Please instantiate the QApplication object first

How do I change the path where R studio is looking , for example RSTUDIO_WHICH_R=/home/kishore/software/R/R-3.4.3/bin/R to new place where I manually installed R 3.4.4

Thanks for your help !!


#2

I don't have an answer, but I have had this before (but in Windows) and I know what caused mine. If I'm using RStudio desktop to work on a project on my corp intranet over VPN, then I close RStudio, close the VPN, then reopen RStudio, I get this behavior. I suspect RStudio tries to open the last project that was open and if that path is no longer available then it hangs...

Maybe try opening a local RStudio project file directly in finder?


#3

Thanks jdlong, I tried it but didnt work , I am trying to change the source file where Rstudio checks for location of bin files. I figured I have installed R 3.4.4 in a different location, I need to say rstudio initiator script to look in the newly installed directory rather than previous directory.


#4

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

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.


#5

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


#6

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)


#7

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.


#8

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.