RStudio is crashing after update on Ubuntu 20.04 (focal)

Hi all,

I've been struggling with this for a couple of weeks so I eventually decided to ask on the community forum.

I've updated my Ubuntu version, R and RStudio (see diagnostics report below). Since the update some of my scripts crash at relatively predictable points. For example, I get the "R session terminated" message when I re-run some lines of code that create a plot (it works fine when I run it the first time). Sometimes the message doesn't show but Rstudio just hangs. Running and rerunning the scripts from

R works fine so I think this issue is related to Rstudio rather than Ubuntu or R. My suspicion: the problem is that the Rstudio version I'm using was built on an older Ubuntu distribution which causes compatibility issues.

Please find below the diagnostics report.

Thanks,
Jens

[1] "1.2.5042"

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

$pdflatex
[1] "/home/jens/bin/pdflatex"

$bibtex
[1] "/home/jens/bin/bibtex"

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

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

$svn
[1] ""

R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.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_4.0.0 tools_4.0.0

SysInfo:
sysname
"Linux"
release
"5.4.0-29-generic"
version
"#33-Ubuntu SMP Wed Apr 29 14:32:27 UTC 2020"
nodename
"roeser"
machine
"x86_64"
login
"jens"
user
"jens"
effective_user
"jens"

R Version:
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 0.0
year 2020
month 04
day 24
svn rev 78286
language R
version.string R version 4.0.0 (2020-04-24)
nickname Arbor Day
$_
[1] "/usr/bin/rstudio"

$_R_CHECK_COMPILATION_FLAGS_KNOWN_
[1] "-Wformat -Werror=format-security -Wdate-time"

$CLICOLOR_FORCE
[1] "1"

$CLUTTER_IM_MODULE
[1] "ibus"

$COLORTERM
[1] "truecolor"

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

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

$DESKTOP_SESSION
[1] "ubuntu"

$DISPLAY
[1] ":1"

$EDITOR
[1] "vi"

$GDMSESSION
[1] "ubuntu"

$GIT_ASKPASS
[1] "rpostback-askpass"

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

$GNOME_SHELL_SESSION_MODE
[1] "ubuntu"

$GNOME_TERMINAL_SCREEN
[1] "/org/gnome/Terminal/screen/2ec3961d_c16c_4314_aecb_ca9140ce4c00"

$GNOME_TERMINAL_SERVICE
[1] ":1.93"

$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/jens"

$IM_CONFIG_PHASE
[1] "1"

$INVOCATION_ID
[1] "69f0ce4a3c034b769a59870942552b0a"

$JOURNAL_STREAM
[1] "9:44947"

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

$LANGUAGE
[1] "en_GB:en"

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

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

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

$LN_S
[1] "ln -s"

$LOGNAME
[1] "jens"

$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:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.zst=01;31:.tzst=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:.wim=01;31:.swm=01;31:.dwm=01;31:.esd=01;31:.jpg=01;35:.jpeg=01;35:.mjpg=01;35:.mjpeg=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"

$MANAGERPID
[1] "1754"

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

$OLDPWD
[1] "/home/jens/Downloads/rstudio/build"

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

$PATH
[1] "/usr/lib/jvm/java-8-openjdk/jre/bin/:/home/jens/.yarn/bin:/home/jens/.config/yarn/global/node_modules/.bin:/home/jens/.local/bin:/home/jens/bin:/opt/texbin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"

$PWD
[1] "/home/jens"

$QT_ACCESSIBILITY
[1] "1"

$QT_IM_MODULE
[1] "ibus"

$QT4_IM_MODULE
[1] "ibus"

$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/4.0"

$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/RtmpdOmmx6"

$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] "27"

$RS_PPM_FD_WRITE
[1] "28"

$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] "80"

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

$RSTUDIO_SESSION_PORT
[1] "33006"

$RSTUDIO_USER_IDENTITY
[1] "jens"

$RSTUDIO_WINUTILS
[1] "bin/winutils"

$SED
[1] "/bin/sed"

$SESSION_MANAGER
[1] "local/roeser:@/tmp/.ICE-unix/2080,unix/roeser:/tmp/.ICE-unix/2080"

$SHELL
[1] "/bin/bash"

$SHLVL
[1] "1"

$SSH_AGENT_PID
[1] "1989"

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

$TAR
[1] "/bin/tar"

$TERM
[1] "xterm-256color"

$USER
[1] "jens"

$USERNAME
[1] "jens"

$VTE_VERSION
[1] "6001"

$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:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop"

$XDG_MENU_PREFIX
[1] "gnome-"

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

$XDG_SESSION_CLASS
[1] "user"

$XDG_SESSION_DESKTOP
[1] "ubuntu"

$XDG_SESSION_TYPE
[1] "x11"

$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-jens.log

19 May 2020 13:49:16 [rsession-jens] 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
19 May 2020 15:36:07 [rsession-jens] 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

RStudio 1.2.5042 does have problems on Ubuntu 20, especially if you have a very high-resolution display (don't know the exact resolution that triggers the problem). Not sure that's the same problem you are seeing, though.

There will be a fix for the Ubuntu 20 crash we know about in an upcoming 1.3 release, but that's not available yet. Very long conversation about it here: https://github.com/rstudio/rstudio/issues/6782

A potential workaround you can try is to launch RStudio from command-line as follows:

export RSTUDIO_CHROMIUM_ARGUMENTS="--disable-seccomp-filter-sandbox"
rstudio
2 Likes

Thanks for your answer, Gary. Apologies for my lack of patience: I've downgraded my ubuntu to bionic beaver and everything is working smoothly now. I encountered problems with other programmes too so abandoning focal seemed to me the fastest (even if not bravest) solution. Sorry for the hassle.

No apologies necessary! I wish we could get the fixes to you faster but we have to juggle a lot of factors to avoid unintentionally breaking something else.

1 Like

I noticed few minutes ago that my last version of openblas-pthread on ubuntu 20.20 was blocking my R session (with or without Rstudio). Need to stop it with kill -9...
Using standard blas/lapack (not openblas) solved the problem.

Note that the openblas policy is to use parallel linear algebra only for some minimum size of matrix. It means that the bug may not occur for small test cases, but only for sufficient matrix sizes.

Hi Gary,

I tried these tips with export, but there was an error, and rstudio crashed. According to the data below.
I use, to test, demo(recursion), in rstudio;clovis@BelaNandaDivo:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04 LTS
Release: 20.04
Codename: focal

What is the suggestion, compile for my platform? I am using the latest package for Ubuntu 18.

clovis@BelaNandaDivo:~ export RSTUDIO_CHROMIUM_ARGUMENTS="--disable-seccomp-filter-sandbox" clovis@BelaNandaDivo:~ rstudio
Warning: QT_DEVICE_PIXEL_RATIO is deprecated. Instead use:
QT_AUTO_SCREEN_SCALE_FACTOR to enable platform plugin controlled per-screen factors.
QT_SCREEN_SCALE_FACTORS to set per-screen factors.
QT_SCALE_FACTOR to set the application global scale factor.
nouveau: kernel rejected pushbuf: No such file or directory
nouveau: ch5: krec 0 pushes 0 bufs 2 relocs 0
nouveau: ch5: buf 00000000 00000002 00000004 00000004 00000000
nouveau: ch5: buf 00000001 00000006 00000004 00000000 00000004
nouveau: kernel rejected pushbuf: No such file or directory
nouveau: ch5: krec 0 pushes 1 bufs 5 relocs 0
nouveau: ch5: buf 00000000 00000005 00000004 00000004 00000000
nouveau: ch5: buf 00000001 00000006 00000004 00000000 00000004
nouveau: ch5: buf 00000002 0000005b 00000004 00000004 00000000
nouveau: ch5: buf 00000003 0000005a 00000002 00000002 00000002
nouveau: ch5: buf 00000004 00000053 00000002 00000000 00000002
nouveau: ch5: psh 00000000 000003d784 000003d894
nouveau: 0x0004a200
nouveau: 0x00000001
nouveau: 0x0004a314
nouveau: 0x00000100
nouveau: 0x0018a21c
nouveau: 0x00000000
nouveau: 0x00000040
nouveau: 0x00000100
nouveau: 0x00000040
nouveau: 0x00000001
nouveau: 0x00000000
nouveau: 0x0008a238
nouveau: 0x00000000
nouveau: 0x00000000
nouveau: 0x0008a30c
nouveau: 0x0032e000
nouveau: 0x0032a000
nouveau: 0x0004a234
nouveau: 0x00000000
nouveau: 0x0010a31c
nouveau: 0x00000100
nouveau: 0x00000040
nouveau: 0x00000101
nouveau: 0x00000000
nouveau: 0x00148200
nouveau: 0x000000d5
nouveau: 0x00000000
nouveau: 0x00000040
nouveau: 0x00000001
nouveau: 0x00000000
nouveau: 0x00108218
nouveau: 0x00000040
nouveau: 0x00000040
nouveau: 0x00000000
nouveau: 0x002cf000
nouveau: 0x00148230
nouveau: 0x000000cf
nouveau: 0x00000000
nouveau: 0x00000040
nouveau: 0x00000001
nouveau: 0x00000000
nouveau: 0x00108248
nouveau: 0x00000040
nouveau: 0x00000040
nouveau: 0x00000000
nouveau: 0x0032a000
nouveau: 0x0004888c
nouveau: 0x00000000
nouveau: 0x001088b0
nouveau: 0x00000000
nouveau: 0x00000000
nouveau: 0x00000040
nouveau: 0x00000040
nouveau: 0x001088c0
nouveau: 0x00000000
nouveau: 0x00000001
nouveau: 0x00000000
nouveau: 0x00000001
nouveau: 0x001088d0
nouveau: 0x00000000
nouveau: 0x00000000
nouveau: 0x00000000
nouveau: 0x00000000
nouveau: 0x00107b00
nouveau: 0x00000000
nouveau: 0x00215000
nouveau: 0x0000026f
nouveau: 0x1000f010
[6963:6963:20200529,135246.724654:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.728008:ERROR ptracer.cc:418] ptrace: No such process (3)
[6962:6962:20200529,135246.728111:ERROR ptracer.cc:441] Unexpected registers size
[6962:6962:20200529,135246.728264:WARNING process_reader_linux.cc:303] Couldn't initialize main thread.
[6962:6962:20200529,135246.728454:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.728714:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.728892:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.728975:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729010:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729041:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729071:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729100:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729130:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729160:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729187:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729214:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729242:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729269:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.729296:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732591:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732660:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732689:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732717:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732745:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732773:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732800:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732828:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732856:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732883:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732911:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.732939:ERROR scoped_ptrace_attach.cc:45] ptrace: Operation not permitted (1)
[6962:6962:20200529,135246.736443:ERROR process_memory_range.cc:86] read out of range
[6962:6962:20200529,135246.736474:ERROR elf_image_reader.cc:558] missing nul-terminator
[6962:6962:20200529,135246.737034:ERROR process_reader_linux.cc:445] no module mappings 0x7fa5e05d4000
[6962:6962:20200529,135246.756796:ERROR elf_dynamic_array_reader.h:61] tag not found
[6962:6962:20200529,135246.757466:ERROR elf_dynamic_array_reader.h:61] tag not found
[6962:6962:20200529,135246.768138:ERROR elf_dynamic_array_reader.h:61] tag not found
[6962:6962:20200529,135246.769814:ERROR elf_dynamic_array_reader.h:61] tag not found
[6962:6962:20200529,135246.776163:ERROR elf_dynamic_array_reader.h:61] tag not found
[6962:6962:20200529,135246.777763:ERROR elf_dynamic_array_reader.h:61] tag not found
[6962:6962:20200529,135246.778009:ERROR elf_dynamic_array_reader.h:61] tag not found
[6962:6962:20200529,135246.778255:ERROR elf_dynamic_array_reader.h:61] tag not found
[6962:6962:20200529,135246.779388:ERROR process_snapshot_linux.cc:100] thread not found 6898
[6962:6962:20200529,135246.781456:ERROR scoped_ptrace_attach.cc:34] ptrace: No such process (3)
Segmentation fault (core dumped)

Best bet is to wait for the first RStudio 1.3 patch release, preview builds should be available very soon. It has the Qt fixes for the (known) problems on newer distros including Ubuntu 20.

You can also give a daily 1.4 build a try (has same fix), but don't recommend those yet for doing actual work.

The issue is in Qt, so yes, compiling yourself with Qt >= 5.12.8 would get the same fix.