Eric Berger
2025-May-19 15:22 UTC
[R] Very odd issue getting "Input/output error" running shiny app from index.html locally but same shiny on my server working fine
[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 at 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 at 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 at 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. >> >[[alternative HTML version deleted]]
Chris Evans
2025-May-19 15:51 UTC
[R] Very odd issue getting "Input/output error" running shiny app from index.html locally but same shiny on my server working fine
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 at tuxedo-os:/run/user/1000# cd doc ??? bash: cd: doc: Permission denied ??? root at tuxedo-os:/run/user/1000# ls doc ??? ls: cannot access 'doc': Permission denied and this: ?? root at 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 at 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 at 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 at 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 at 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>
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