[R] Very odd issue getting "Input/output error" running shiny app from index.html locally but same shiny on my server working fine
Chris Evans
chr|@ho|d @end|ng |rom p@yctc@org
Mon May 19 17:51:01 CEST 2025
Oooh thanks. I should probably have thought of that: this list is
brilliant when my brain goes on strike.
OK, it's http://127.0.0.1:5071 for me and using the "view the page with
the system web browser" when I have the index.html page opened via
Rstudio has the system browser point to
file:///run/user/1000/doc/9065bcbf/index.html and if I click on the link
to the app it goes to
file:///run/user/1000/doc/9065bcbf/apps/COREpapers1 and says "Your file
couldn’t be accessed"
Then if I open a console with root privileges I get to this:
root using tuxedo-os:/run/user/1000# cd doc
bash: cd: doc: Permission denied
root using tuxedo-os:/run/user/1000# ls doc
ls: cannot access 'doc': Permission denied
and this:
root using tuxedo-os:/run/user# ls -lsart
total 0
0 drwxr-xr-x 3 root root 60 May 19 15:36 .
0 drwx------ 21 chris chris 660 May 19 16:42 1000
0 drwxr-xr-x 43 root root 1160 May 19 16:46 ..
and
root using tuxedo-os:/run/user/1000# ls -lsart
ls: cannot access 'doc': Permission denied
ls: cannot access 'gvfs': Permission denied
total 12
? d????????? ? ? ? ? ? gvfs
? d????????? ? ? ? ? ? doc
0 srw-rw-rw- 1 chris chris 0 May 19 15:36 bus
0 drwx------ 2 chris chris 60 May 19 15:36 gcr
0 srw------- 1 chris chris 0 May 19 15:36 drkonqi-coredump-launcher
0 drwxr-xr-x 2 chris chris 60 May 19 15:36 speech-dispatcher
0 srw-rw-rw- 1 chris chris 0 May 19 15:36 snapd-session-agent.socket
0 srw-rw-rw- 1 chris chris 0 May 19 15:36 pk-debconf-socket
0 srw-rw-rw- 1 chris chris 0 May 19 15:36 pipewire-0-manager
0 srw-rw-rw- 1 chris chris 0 May 19 15:36 pipewire-0
0 drwx------ 2 chris chris 160 May 19 15:36 gnupg
0 drwx------ 3 chris chris 60 May 19 15:36 dbus-1
0 -rw-rw---- 1 chris chris 0 May 19 15:36 pipewire-0-manager.lock
0 -rw-rw---- 1 chris chris 0 May 19 15:36 pipewire-0.lock
0 drwx------ 2 chris chris 80 May 19 15:36 pulse
0 drwx------ 2 chris chris 80 May 19 15:36 keyring
0 srwxrwxr-x 1 chris chris 0 May 19 15:36 kwallet5.socket
0 drwx------ 2 chris chris 40 May 19 15:36 gvfsd
0 drwx------ 2 chris chris 60 May 19 15:36 dconf
0 drwx------ 2 chris chris 60 May 19 15:36 at-spi
4 -rw-rw-r-- 1 chris chris 77 May 19 15:36 KSMserver__0
4 -rw------- 1 chris chris 330 May 19 15:36 iceauth_RTpbEQ
0 drwxr-xr-x 7 chris chris 180 May 19 15:36 systemd
0 drwxrwxr-x 2 chris chris 60 May 19 15:36 Nextcloud
0 drwxr-xr-x 3 root root 60 May 19 15:36 ..
0 drwx------ 3 chris chris 80 May 19 15:39 .flatpak-helper
4 -rw------- 1 chris chris 99 May 19 15:40 .Xauthority
0 drwx------ 3 chris chris 60 May 19 15:40 snap.thunderbird
0 drwx------ 4 chris chris 80 May 19 15:43 app
0 drwx------ 3 chris chris 60 May 19 15:51 .ecore
0 drwxr-xr-x 10 chris chris 200 May 19 16:37 .flatpak
0 drwxr-xr-x 2 chris chris 160 May 19 16:37 .dbus-proxy
0 drwx------ 21 chris chris 660 May 19 16:42 .
So I think this confirms that this is an OS issue and something is
putting /run/user/1000/doc off limits even for root though
/run/user/1000 is open at least to root and presumably
I can see I am now way off piste here but if anyone has any
suggestions, even about the likely best places to take this next, I
would appreciate it.
Many thanks Eric and all (I have learned SO much from this list over hm,
well I have kept messages going back nine years but I know it's much
longer back than that!)
Chris
On 19/05/2025 16:22, Eric Berger wrote:
> [forgot to hit reply-all]
> Hi Chris,
> When I have encountered similar sounding problems in the past I was
> able to work around them as follows.
> Instead of running rstudio locally, I run rstudio-server locally and
> then in a browser I enter the URL http://localhost:8787/
>
> HTH,
> Eric
>
>
> On Mon, May 19, 2025 at 6:21 PM Eric Berger <ericjberger using gmail.com> wrote:
>
> Hi Chris,
> When I have encountered similar sounding problems in the past I
> was able to work around them as follows.
> Instead of running rstudio locally, I run rstudio-server locally
> and then in a browser I enter the URL http://localhost:8787/
>
> HTH,
> Eric
>
> On Mon, May 19, 2025 at 6:01 PM Chris Evans via R-help
> <r-help using r-project.org> wrote:
>
> I realise that shiny and Rstudio is often seen as OT here but
> I have a
> strong suspicion that the issue is R or R/OS related so I hope
> someone
> here will have some thoughts that might help me.
>
> The scenario is that as of yesterday running my shiny project
> locally
> from within Rtudio, i.e. by opening the index.html with
> preview, gets me
> "Input/output error" when I click on a link to an app.
>
> The same shiny running on my server (https://shiny.psyctc.org)
> runs
> fine. So if I click on the link
> https://shiny.psyctc.org/apps/COREpapers1 there then that app
> runs
> fine. However, when I do the same locally I get "Input/output
> error" in
> the window that pops up where the app should run! Very
> bizarrely, if I
> open the app itself locally in Rstudio it runs fine.
>
> I am completely baffled by this, have never seen it before and
> some
> searching on the web only suggest that "Input/output error"
> may be an OS
> level error and a suggestion that dmesg may give me a clue
> about it.
> However,dmesg is showing nothing that looks remotely pertinent
> and
> nothing new appears in rerunning dmesg immediately after
> invoking that
> error message. I have updated and rebooted the local machine
> (rather
> desperate I admit) and that did update quite a lot of core
> linux files
> (despite my having updated this morning say six hours ago) ...
> but
> nothing new in R or R packages and the problem stayed the same.
>
> To make it even more confusing the server and the local
> machine are both
> running R 4.5.0 (2025-04-11) and shiny version is 1.10.0 on
> both. I use
> git to package the server project and that gets transferred to
> the
> server from the local machine and commit is showing no local
> changes and
> the last change is showing as on 5.v.25. The project can be
> seen at
> https://github.com/cpsyctc/shiny-server.
>
> The server is running
> Debian 5.10.197-1 (2023-09-29) x86_64 GNU/Linux
> but the local machine runs
> Linux tuxedo-os 6.11.0-114025-tuxedo #25~24.04.1tux1 SMP
> PREEMPT_DYNAMIC
>
> I would hugely appreciate it if anyone has any thoughts about
> this, any
> things I might do to debug it more. It's currently getting in
> the way of
> some mildly urgent work I need to do on the server (of course
> it is, IT
> knows when you are vulnerable!)
>
> TIA,
>
> Chris
>
> --
> Chris Evans (he/him)
> Visiting Professor, UDLA, Quito, Ecuador
> CORE site: http://www.coresystemtrust.org.uk
> <https://www.coresystemtrust.org.uk/>
> Other work web site: https://www.psyctc.org/psyctc/
> Personal site: https://www.psyctc.org/pelerinage2016/
> <https://ombook.psyctc.org/book>
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> https://www.R-project.org/posting-guide.html
> <https://www.R-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
--
Chris Evans (he/him)
Visiting Professor, UDLA, Quito, Ecuador
CORE site: http://www.coresystemtrust.org.uk
<https://www.coresystemtrust.org.uk/>
Other work web site: https://www.psyctc.org/psyctc/
Personal site: https://www.psyctc.org/pelerinage2016/
<https://ombook.psyctc.org/book>
More information about the R-help
mailing list