After pacman -Syu RStudio stopped opening


I updated my system using pacman -Syu on 2020-11-06 and now rstudio-desktop-bin (most recent version from AUR, , v1.3.1093-1) does not open consistently. Sometimes it opens a window then closes it immediately, sometimes it’s a black window, and sometimes it opens a window and appears normal but crashes in short order. Anyone else having this problem?

inxi -Fazy:

  Kernel: 5.8.18-1-MANJARO x86_64 bits: 64 compiler: gcc v: 10.2.0 
  parameters: BOOT_IMAGE=/boot/vmlinuz-5.8-x86_64 
  root=UUID=b6fb2e8b-3700-4370-94dc-da42962edaa6 rw quiet apparmor=1 
  security=apparmor udev.log_priority=3 
  Desktop: Xfce 4.14.2 tk: Gtk 3.24.20 info: xfce4-panel wm: xfwm4 
  dm: LightDM 1.30.0 Distro: Manjaro Linux 
  Type: Desktop System: ASUSTeK product: N/A v: N/A serial: <filter> 
  Mobo: ASUSTeK model: WS C246 PRO v: Rev 1.xx serial: <filter> 
  UEFI: American Megatrends v: 0802 date: 11/30/2018 
  Info: 8-Core model: Intel Core i9-9900K bits: 64 type: MT MCP 
  arch: Kaby Lake family: 6 model-id: 9E (158) stepping: C (12) microcode: D6 
  L2 cache: 16.0 MiB 
  flags: avx avx2 lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 bogomips: 115232 
  Speed: 800 MHz min/max: 800/5000 MHz Core speeds (MHz): 1: 800 2: 800 3: 800 
  4: 800 5: 801 6: 800 7: 800 8: 800 9: 800 10: 800 11: 800 12: 800 13: 800 
  14: 800 15: 801 16: 800 
  Vulnerabilities: Type: itlb_multihit status: KVM: VMX unsupported 
  Type: l1tf status: Not affected 
  Type: mds mitigation: Clear CPU buffers; SMT vulnerable 
  Type: meltdown status: Not affected 
  Type: spec_store_bypass 
  mitigation: Speculative Store Bypass disabled via prctl and seccomp 
  Type: spectre_v1 
  mitigation: usercopy/swapgs barriers and __user pointer sanitization 
  Type: spectre_v2 mitigation: Full generic retpoline, IBPB: conditional, 
  IBRS_FW, STIBP: conditional, RSB filling 
  Type: srbds mitigation: Microcode 
  Type: tsx_async_abort mitigation: Clear CPU buffers; SMT vulnerable 
  Device-1: NVIDIA TU106 [GeForce RTX 2070] vendor: PNY driver: nouveau 
  v: kernel bus ID: 01:00.0 chip ID: 10de:1f02 
  Display: x11 server: X.Org 1.20.9 driver: modesetting,nouveau 
  alternate: fbdev,nv,vesa display ID: :0.0 screens: 1 
  Screen-1: 0 s-res: 7680x2160 s-dpi: 96 s-size: 2032x571mm (80.0x22.5") 
  s-diag: 2111mm (83.1") 
  Monitor-1: DP-1 res: 3840x2160 hz: 60 dpi: 163 size: 600x340mm (23.6x13.4") 
  diag: 690mm (27.2") 
  Monitor-2: HDMI-1 res: 3840x2160 hz: 60 dpi: 163 
  size: 600x340mm (23.6x13.4") diag: 690mm (27.2") 
  OpenGL: renderer: NV166 v: 4.3 Mesa 20.2.1 direct render: Yes 
  Device-1: Intel Cannon Lake PCH cAVS vendor: ASUSTeK driver: snd_hda_intel 
  v: kernel alternate: snd_soc_skl,snd_sof_pci bus ID: 00:1f.3 
  chip ID: 8086:a348 
  Device-2: NVIDIA TU106 High Definition Audio vendor: PNY 
  driver: snd_hda_intel v: kernel bus ID: 01:00.1 chip ID: 10de:10f9 
  Sound Server: ALSA v: k5.8.18-1-MANJARO 
  Device-1: Intel Ethernet I219-LM vendor: ASUSTeK driver: e1000e v: 3.2.6-k 
  port: efa0 bus ID: 00:1f.6 chip ID: 8086:15bb 
  IF: eno1 state: down mac: <filter> 
  Device-2: Broadcom and subsidiaries BCM4352 802.11ac Wireless Network Adapter vendor: ASUSTeK driver: wl v: kernel modules: bcma port: 4000 
  bus ID: 04:00.0 chip ID: 14e4:43b1 
  IF: wlp4s0 state: up mac: <filter> 
  Device-3: Intel I210 Gigabit Network vendor: ASUSTeK driver: igb v: 5.6.0-k 
  port: 3000 bus ID: 06:00.0 chip ID: 8086:1533 
  IF: enp6s0 state: down mac: <filter> 
  IF-ID-1: docker0 state: down mac: <filter> 
  Local Storage: total: 14.60 TiB used: 679.02 GiB (4.5%) 
  SMART Message: Required tool smartctl not installed. Check --recommends 
  ID-1: /dev/nvme0n1 vendor: Intel model: SSDPEKNW020T8 size: 1.86 TiB 
  block size: physical: 512 B logical: 512 B speed: 31.6 Gb/s lanes: 4 
  serial: <filter> rev: 002C scheme: GPT 
  ID-2: /dev/sda vendor: Seagate model: ST8000DM004-2CX188 size: 7.28 TiB 
  block size: physical: 4096 B logical: 512 B speed: 6.0 Gb/s 
  rotation: 5425 rpm serial: <filter> rev: 0001 scheme: MBR 
  ID-3: /dev/sdb type: USB vendor: Western Digital model: WD Elements 25A3 
  size: 5.46 TiB block size: physical: 4096 B logical: 512 B serial: <filter> 
  rev: 1021 scheme: GPT 
  ID-1: / raw size: 1.86 TiB size: 1.83 TiB (98.38%) used: 679.02 GiB (36.2%) 
  fs: ext4 dev: /dev/nvme0n1p2 
  Kernel: swappiness: 60 (default) cache pressure: 100 (default) 
  ID-1: swap-1 type: file size: 31.25 GiB used: 0 KiB (0.0%) priority: -2 
  file: /swap/swapfile 
  System Temperatures: cpu: 27.8 C mobo: N/A gpu: nouveau temp: 46.0 C 
  Fan Speeds (RPM): N/A gpu: nouveau fan: 657 
  Processes: 309 Uptime: 8m Memory: 62.68 GiB used: 2.47 GiB (3.9%) 
  Init: systemd v: 246 Compilers: gcc: 10.2.0 clang: 10.0.1 Packages: 
  pacman: 1255 lib: 371 flatpak: 0 Shell: Bash v: 5.0.18 
  running in: xfce4-terminal inxi: 3.1.08 



If you havent rebuilt your AUR package against current system libs then thats why.

1 Like

@cscs thanks but I installed the latest rstudio-desktop-bin from AUR after I did the system update

Hm. What happens if you launch it from terminal? Any clues?

Maybe something here! When I launch from terminal and it crashes, I see many lines of “nouveau: memory address” then this error. But sometimes it freezes everything and I have to force reboot.

nouveau: 	0x001f001e
nouveau: 	0x0020001f
nouveau: 	0x00210020
nouveau: 	0x00230022
nouveau: 	0x80000585
nouveau: 	0x200406c0
nouveau: 	0x00000000
nouveau: 	0x00014000
nouveau: 	0x000004f9
nouveau: 	0x1000f010
[3202:3203:20201109,161157.589632:ERROR] open /home/mcsimenc/.r/crashpad_database/pending/0aa2ed44-3856-4a36-adc5-e852ff28e890.lock: File exists (17)
[3202:3202:20201109,161157.591859:ERROR] read out of range
[3202:3202:20201109,161157.591865:ERROR] missing nul-terminator
[3202:3202:20201109,161157.591983:ERROR] no module mappings 0x7f737a0fd000
[3202:3202:20201109,161157.593840:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.593996:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.595087:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.595128:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.595943:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.595974:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.596004:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.596033:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.596064:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.596120:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.596151:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.596179:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3202:20201109,161157.596209:ERROR elf_dynamic_array_reader.h:61] tag not found
[3202:3203:20201109,161157.598011:ERROR] opendir: No such file or directory (2)
Segmentation fault (core dumped)

That won’t help because you just reinstalled the same binary files that were built against older libraries. Build rstudio-desktop or rstudio-desktop-git and you should be good to go.

Awesome thanks @Yochanan.

I installed rstudio-desktop but RStudio doesn’t work: it loads but the main part of the window remains blank.

I also tried to build rstudio-desktop-git but got this error:

CMake Error at src/cpp/session/CMakeLists.txt:30 (message):
  pandoc not found (re-run install-dependencies script to install)

However the most recent pandoc in the Arch repository is older than that, version

Not sure what to tell you then. It could be an upstream issue. Have you poked the internet? :wink:

We don’t even have that in the Manjaro unstable branch yet. Arch just updated to today. They may be holding it back to avoid breakage with packages that depend on it.

I’ll do some more poking around

Ok, thanks for your help!

Might be a bit of a shot in the dark, but have you tried removing RStudio’s cache and config files (plus any other crud it leaves around the home directory)?

I’m currently using the latest rstudio-desktop-bin from the AUR without issue. Looking at your inxi output the main differences between our systems that ‘might’ make a difference are GFX card manufacturers (Intel + AMD vs Nvidia), desktop environment (Gnome vs XFCE), desktop session type (Wayland vs X11), kernel version (5.9 vs 5.8) and monitor resolution (2 x 1080p vs 2 x 4K). Not sure if that’s helpful or not, but might give some clues if removing the config/cache stuff doesn’t help.

Otherwise, have you checked the comments in the AUR?

Thanks Freakster!

Yeah, removing the config/cache directory didn’t affect the problem.

I tried installing kernel v5.9 using mhwd-kernel -i linux59 because pacman -S linux installs v5.8 even though v5.9.6 is the latest in the Arch repository. Changing my monitor resolution didn’t change RStudio’s behavior either. I’m under the impression that I can’t use Wayland with XFCE.

I tried to install Gnome using pacman -S gnome but I think it tells me I have gdm-dev installed and also that gdm-dev conflicts with libgdm-dev. But pacman -R gdm and pacman -R gdm-dev report target not found.

looking for conflicting packages...
warning: removing 'gdm' from target list because it conflicts with 'gdm-dev'
error: unresolvable package conflicts detected
error: failed to prepare transaction (conflicting dependencies)
:: gdm-dev and libgdm-dev are in conflict

I didn’t see anything relevant in the AUR comments.

pacman -Qs gdm

I reinstalled Manjaro with Gnome and I haven’t had this problem since.

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Don’t want to be the naysayer, but this isn’t a SOLUTION.

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