Hi everyone,
I am currently having trouble using Rstudio. Everything works fine until I click on the file outlets, then it freezes with the "Rstudio does not respond" error message. Even if I am not creating/saving a new file/project it happens each time I use the file button.
I have already removes the ~/.rstudio-desktop
and ~/.config/RStudio
folders....
Does anyone have already have a similar issue ?
Thanks you in advance for your advice,
Clément
PS: Here is my rstudio-diagnostic-report file :
[1] "1.1.453"
$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] "/usr/bin/svn"
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /bioinfo/local/build/Centos/R/R-3.5.0/lib64/R/lib/libRblas.so
LAPACK: /bioinfo/local/build/Centos/R/R-3.5.0/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.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_3.5.0 tools_3.5.0
SysInfo:
sysname release
"Linux" "3.10.0-862.11.6.el7.x86_64"
version nodename
"#1 SMP Tue Aug 14 21:49:04 UTC 2018" "u900-bdd-1-198n-6985.curie.fr"
machine login
"x86_64" "cbenoit"
user effective_user
"cbenoit" "cbenoit"
R Version:
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 5.0
year 2018
month 04
day 23
svn rev 74626
language R
version.string R version 3.5.0 (2018-04-23)
nickname Joy in Playing
$`_`
[1] "/bioinfo/local/build/Centos/R/rstudio/rstudio"
$`BASH_FUNC_module()`
[1] "() { eval `/usr/bin/modulecmd bash $*`\n}"
$BOLD
[1] "\\e[1m"
$BOWTIE_INDEXES
[1] "/data/annotations/bowtie_indexes/"
$CLICOLOR_FORCE
[1] "1"
$COBBLER_SERVER
[1] "kickstart.curie.fr"
$COLORTERM
[1] "truecolor"
$DBUS_SESSION_BUS_ADDRESS
[1] "unix:abstract=/tmp/dbus-BO8Fs7q4TX,guid=56bad48780b230d11bd277655d4415cd"
$DEF
[1] "\\e[0;0m"
$DESKTOP_SESSION
[1] "gnome-classic"
$DISPLAY
[1] ":0"
$EDITOR
[1] "vi"
$ftp_proxy
[1] "http://www-cache:3128"
$FTP_PROXY
[1] "http://www-cache:3128"
$GDM_LANG
[1] "fr_FR.UTF-8"
$GDMSESSION
[1] "gnome-classic"
$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] "classic"
$HDF5_DIR
[1] "/bioinfo/users/cbenoit/Apps/hdf5/bin/"
$HISTCONTROL
[1] "ignoredups"
$HISTSIZE
[1] "1000"
$HOME
[1] "/data/users/cbenoit"
$HOSTNAME
[1] "u900-bdd-1-198n-6985.curie.fr"
$http_proxy
[1] "http://www-cache.curie.fr:3128"
$HTTP_PROXY
[1] "http://www-cache.curie.fr:3128"
$https_proxy
[1] "http://www-cache:3128"
$HTTPS_PROXY
[1] "http://www-cache:3128"
$IMSETTINGS_INTEGRATE_DESKTOP
[1] "yes"
$IMSETTINGS_MODULE
[1] "none"
$KDEDIRS
[1] "/usr"
$LANG
[1] "fr_FR.UTF-8"
$LD_LIBRARY_PATH
[1] "/bioinfo/local/build/Centos/R/R-3.5.0/lib64/R/lib::/lib:/usr/local/lib64:/usr/lib/jvm/java-1.8.0-openjdk/jre/lib/amd64/server"
$LESSOPEN
[1] "||/usr/bin/lesspipe.sh %s"
$LN_S
[1] "ln -s"
$LOADEDMODULES
[1] ""
$LOGNAME
[1] "cbenoit"
$LS_COLORS
[1] "rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:"
$MAIL
[1] "/var/spool/mail/cbenoit"
$MAKE
[1] "make"
$MODULEPATH
[1] "/usr/share/Modules/modulefiles:/etc/modulefiles"
$MODULESHOME
[1] "/usr/share/Modules"
$no_proxy
[1] "localhost,127.0.0.0/8,10.0.0.0/8,.curie.fr,.curie.u-psud.fr,.curie.net"
$PAGER
[1] "/usr/bin/less"
$PATH
[1] "/bioinfo/local/build/Centos/tabix/tabix-0.2.5/:/bioinfo/local/build/Centos/R/rstudio/:/bioinfo/users/cbenoit/Documents/Tools/msisensor:/bioinfo/users/cbenoit/Apps/hdf5/bin/:/bioinfo/local/build/Centos/bowtie2-2.2.5/:/bioinfo/local/build/Centos/samtools/samtools-1.3/bin/:/usr/bin/:/bioinfo/local/Centos/BEDTools/bin/:/bioinfo/local/build/Centos/python/python-2.7.12/bin/:/bioinfo/local/build/Centos/python/python-3.5.2/bin/:/bioinfo/local/build/Centos/python/python-2.7.12/bin:/usr/local/bin:/usr/bin:/bin:/data/kdi_prod/bin/:/bioinfo/pipelines/kdi_fs/bin/"
$PERL5LIB
[1] "/bioinfo/users/cbenoit/Apps/perl_modules/lib/perl5/"
$proxy
[1] "http://www-cache:3128"
$PROXY
[1] "http://www-cache:3128"
$PWD
[1] "/bioinfo/users/cbenoit"
$QT_GRAPHICSSYSTEM_CHECKED
[1] "1"
$QT_IM_MODULE
[1] "xim"
$QT_PLUGIN_PATH
[1] "/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins"
$QTDIR
[1] "/usr/lib64/qt-3.3"
$QTINC
[1] "/usr/lib64/qt-3.3/include"
$QTLIB
[1] "/usr/lib64/qt-3.3/lib"
$R_BROWSER
[1] "/usr/bin/firefox"
$R_BZIPCMD
[1] "/usr/bin/bzip2"
$R_DOC_DIR
[1] "/bioinfo/local/build/Centos/R/R-3.5.0/lib64/R/doc"
$R_GZIPCMD
[1] "/usr/bin/gzip"
$R_HOME
[1] "/bioinfo/local/build/Centos/R/R-3.5.0/lib64/R"
$R_INCLUDE_DIR
[1] "/bioinfo/local/build/Centos/R/R-3.5.0/lib64/R/include"
$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] "lpr"
$R_RD4PDF
[1] "times,inconsolata,hyper"
$R_SESSION_TMPDIR
[1] "/tmp/RtmpYpOztw"
$R_SHARE_DIR
[1] "/bioinfo/local/build/Centos/R/R-3.5.0/lib64/R/share"
$R_SYSTEM_ABI
[1] "linux,gcc,gxx,gfortran,?"
$R_TEXI2DVICMD
[1] "texi2dvi"
$R_UNZIPCMD
[1] "/usr/bin/unzip"
$R_ZIPCMD
[1] "/usr/bin/zip"
$RMARKDOWN_MATHJAX_PATH
[1] "/bioinfo/local/build/Centos/R/rstudio/rstudio-1.1.453/resources/mathjax-26"
$RS_LOCAL_PEER
[1] "/tmp/20364-rsession"
$RS_PPM_FD_READ
[1] "11"
$RS_PPM_FD_WRITE
[1] "12"
$RS_RPOSTBACK_PATH
[1] "/bioinfo/local/build/Centos/R/rstudio/rstudio-1.1.453/bin/rpostback"
$RS_SHARED_SECRET
[1] "16816927778469308861804289383"
$RSTUDIO
[1] "1"
$RSTUDIO_CONSOLE_COLOR
[1] "256"
$RSTUDIO_CONSOLE_WIDTH
[1] "80"
$RSTUDIO_PANDOC
[1] "/bioinfo/local/build/Centos/R/rstudio/rstudio-1.1.453/bin/pandoc"
$RSTUDIO_SESSION_PORT
[1] "20364"
$RSTUDIO_USER_IDENTITY
[1] "cbenoit"
$RSTUDIO_WHICH_R
[1] "/bioinfo/local/build/Centos/R/R-3.5.0/bin/R"
$RSTUDIO_WINUTILS
[1] "bin/winutils"
$SED
[1] "/usr/bin/sed"
$SESSION_MANAGER
[1] "local/unix:@/tmp/.ICE-unix/13958,unix/unix:/tmp/.ICE-unix/13958"
$SHELL
[1] "/bin/bash"
$SHLVL
[1] "2"
$SSH_AGENT_PID
[1] "14137"
$SSH_AUTH_SOCK
[1] "/run/user/7629/keyring/ssh"
$TAR
[1] "/usr/bin/gtar"
$TERM
[1] "xterm-256color"
$UNDER
[1] "\\e[4m"
$USER
[1] "cbenoit"
$USERNAME
[1] "cbenoit"
$VTE_VERSION
[1] "4602"
$WINDOWID
[1] "41951261"
$WINDOWPATH
[1] "1"
$XAUTHORITY
[1] "/run/gdm/auth-for-cbenoit-83fb3v/database"
$XDG_CURRENT_DESKTOP
[1] "GNOME-Classic:GNOME"
$XDG_MENU_PREFIX
[1] "gnome-"
$XDG_RUNTIME_DIR
[1] "/run/user/7629"
$XDG_SEAT
[1] "seat0"
$XDG_SESSION_DESKTOP
[1] "gnome-classic"
$XDG_SESSION_ID
[1] "1"
$XDG_SESSION_TYPE
[1] "x11"
$XDG_VTNR
[1] "1"
$XMODIFIERS
[1] "@im=none"
[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
--------------------------------------------------
02 Aug 2019 11:19:13 [rdesktop] ERROR system error 104 (Connexion ré-initialisée par le correspondant); OCCURRED AT: void rstudio::core::http::AsyncClient<SocketService>::handleReadStatusLine(const rstudio_boost::system::error_code&) [with SocketService = rstudio_boost::asio::basic_stream_socket<rstudio_boost::asio::local::stream_protocol>] /home/fedora/rstudio/src/cpp/core/include/core/http/AsyncClient.hpp:376; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) /home/fedora/rstudio/src/cpp/desktop/DesktopNetworkReply.cpp:288
02 Aug 2019 12:04:56 [rdesktop] WARNING R include path (/usr/include/R) not found; LOGGED FROM: bool core::r_util::<unnamed>::validateREnvironment(const core::r_util::EnvironmentVars&, const core::FilePath&, std::string*) /root/rstudio/src/cpp/core/r_util/REnvironmentPosix.cpp:390
Log file: rsession-cbenoit.log
--------------------------------------------------
02 Aug 2019 11:21:33 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:25:19 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:25:52 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:26:53 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:27:48 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:32:09 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:34:36 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:47:30 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:49:03 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:49:44 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:54:02 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:55:05 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 11:59:49 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 12:00:43 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239
02 Aug 2019 12:02:14 [rsession-cbenoit] ERROR Parent terminated; LOGGED FROM: void {anonymous}::detectParentTermination() /home/fedora/rstudio/src/cpp/session/SessionMain.cpp:1239