Task #3181

BlueBRIDGE - Project WP #629: WP4 - VREs Deployment and Operation [Months: 1-30]

BlueBRIDGE - Project Task #630: T4.1 BlueBRIDGE Infrastructure Operation [Months: 1-30]

Update RStudio on rstudio.d4science.org

Added by Gianpaolo Coro over 3 years ago. Updated over 3 years ago.

Status:ClosedStart date:Apr 11, 2016
Priority:UrgentDue date:Apr 15, 2016
Assignee:_InfraScience Systems Engineer% Done:

100%

Category:High-Throughput-Computing
Sprint:External Tools
Infrastructure:Development, Production
Milestones:
Duration: 5

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)

History

#1 Updated by Andrea Dell'Amico over 3 years ago

  • Assignee changed from Andrea Dell'Amico to _InfraScience Systems Engineer

#2 Updated by Pasquale Pagano over 3 years ago

  • 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.

#3 Updated by Andrea Dell'Amico over 3 years ago

  • 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.

#4 Updated by Andrea Dell'Amico over 3 years ago

  • Due date set to Apr 15, 2016

GP is asking to complete the upgrade not later than Friday 15th.

#5 Updated by Gabriele Giammatteo over 3 years ago

I see #630 more appropriate as parent task for this ticket. If you agree, please update it

#6 Updated by Gianpaolo Coro over 3 years ago

  • Parent task changed from #698 to #630

#7 Updated by Massimiliano Assante over 3 years ago

  • Tracker changed from Support to Task

#8 Updated by Andrea Dell'Amico over 3 years ago

  • Status changed from New to In Progress

#9 Updated by Andrea Dell'Amico over 3 years ago

  • % 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.

#10 Updated by Andrea Dell'Amico over 3 years ago

@gianpaolo.coro@isti.cnr.it did you have the time to test if rstudio server is working on rstudio-dev.d4science.org?

#11 Updated by Gianpaolo Coro over 3 years ago

I cannot access to rstudio-dev.d4science.org. Both TabMan and direct access to the RStudio url send me to http://rstudio-dev.d4science.org/r-connector/gcube/service/disconnect , which says that I'm disconnected. Perhaps this requires updating the RStudio Connector. @lucio.lelii@isti.cnr.it could you please give it a look?

#12 Updated by Lucio Lelii over 3 years ago

The problem seems related to the configuration of Rstudio server with LDAP. @tommaso.piccioli@isti.cnr.it is checking what happened.

#13 Updated by Tommaso Piccioli over 3 years ago

Could you please test rstudio-dev from the portal?

#14 Updated by Gianpaolo Coro over 3 years ago

It works both via TabMan and via portal now.

#15 Updated by Andrea Dell'Amico over 3 years ago

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?

#16 Updated by Gianpaolo Coro over 3 years ago

Yes, it works.

#17 Updated by Andrea Dell'Amico over 3 years ago

Let us know when the production server can be upgraded, then.

#18 Updated by Gianpaolo Coro over 3 years ago

The infrastructure upgrade of today would be the best moment.

#19 Updated by Andrea Dell'Amico over 3 years ago

OK

#20 Updated by Andrea Dell'Amico over 3 years ago

  • % Done changed from 60 to 100
  • Status changed from In Progress to Feedback

The production server is now running rstudio-server-0.99.902

#21 Updated by Andrea Dell'Amico over 3 years ago

It seems that after the upgrade the option

auth-minimum-user-id=1000

is needed inside /etc/rserver/rserver.conf

#22 Updated by Gianpaolo Coro over 3 years ago

  • Status changed from Feedback to Closed

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