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@tuxedo-os:/run/user/1000# cd doc
bash: cd: doc: Permission denied
root@tuxedo-os:/run/user/1000# ls doc
ls: cannot access 'doc': Permission denied
and this:
root@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@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 <ericjber...@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@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@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>
______________________________________________
R-help@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
and provide commented, minimal, self-contained, reproducible code.
