Task #3181
closed
Update RStudio on rstudio.d4science.org
Added by Gianpaolo Coro about 9 years ago.
Updated almost 9 years ago.
Assignee:
_InfraScience Systems Engineer
Category:
High-Throughput-Computing
Infrastructure:
Development, Production
Description
There is a discrepancy between the RStudio installation and the R installation. When starting the RStudio interface on http://rstudio.d4science.org/ the following error occurs:
Error in tools:::httpdPort > 0L :
comparison (6) is possible only for atomic and list types
11 Apr 2016 13:57:35 [rsession-gianpaolo.coro] ERROR r error 4 (R code execution error) [errormsg=Error in tools:::httpdPort > 0L :
comparison (6) is possible only for atomic and list types
]; OCCURRED AT: core::Error r::exec::<unnamed>::evaluateExpressionsUnsafe(SEXPREC*, SEXPREC*, SEXPREC**, r::sexp::Protect*) /home/ubuntu/rstudio/src/cpp/r/RExec.cpp:148; LOGGED FROM: core::Error session::modules::help::initialize() /home/ubuntu/rstudio/src/cpp/session/modules/SessionHelp.cpp:892
Which is probably due to an obsolete version of RStudio (see http://r.789695.n4.nabble.com/Warning-message-when-starting-RStudio-td4706292.html)
- Assignee changed from Andrea Dell'Amico to _InfraScience Systems Engineer
- Priority changed from Normal to Immediate
Tomorrow there will be a course in Pisa lasting on Thursday. This is one of the service that will be used. I think it is urgent to fix this issue. Thanks.
- Priority changed from Immediate to Urgent
- Infrastructure Development added
Gianpaolo does not need an updated rstudio.d4science.org for his teaching. Let's proceed this way
- update R and rstudio-server on rstudio-dev.d4science.org, and test that it works without errors (automate the rstudio-server installation procedure)
- When rstudio-dev.d4science.org works, update rstudio.d4science.org the same way
Note that I added 2 additional GB of RAM to the rstudio.d4science.org VM because I've seen OOM errors in the logs. They are old, but all the memory is used right now. The VM need to be shutdown/restarted to see the additional memory.
- Due date set to Apr 15, 2016
GP is asking to complete the upgrade not later than Friday 15th.
I see #630 more appropriate as parent task for this ticket. If you agree, please update it
- Parent task changed from #698 to #630
- Tracker changed from Support to Task
- Status changed from New to In Progress
- % Done changed from 0 to 60
rstudio-dev.d4science.org is now running rstudio-server 0.99 and R 3.2.3 with the same set of R plugins that are currently installed on rstudio.d4science.org.
@gianpaolo.coro@isti.cnr.it did you have the time to test if rstudio server is working on rstudio-dev.d4science.org
?
The problem seems related to the configuration of Rstudio server with LDAP. @tommaso.piccioli@isti.cnr.it is checking what happened.
Could you please test rstudio-dev from the portal?
It works both via TabMan and via portal now.
Gianpaolo Coro wrote:
It works both via TabMan and via portal now.
@gianpaolo.coro@isti.cnr.it Did you also check if the server works well with the new version of R?
Let us know when the production server can be upgraded, then.
The infrastructure upgrade of today would be the best moment.
- Status changed from In Progress to Feedback
- % Done changed from 60 to 100
The production server is now running rstudio-server-0.99.902
It seems that after the upgrade the option
auth-minimum-user-id=1000
is needed inside /etc/rserver/rserver.conf
- Status changed from Feedback to Closed
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