Task #3181: Update RStudio on rstudio.d4science.org - D4Science Infrastructure - D4science

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Task #3181

closed

Update RStudio on rstudio.d4science.org

Added by Gianpaolo Coro about 9 years ago. Updated almost 9 years ago.

Status:

Closed

Priority:

Urgent

Assignee:

_InfraScience Systems Engineer

Category:

High-Throughput-Computing

Target version:

External Tools

Start date:

Apr 11, 2016

Due date:

Apr 15, 2016

% Done:

100%

Estimated time:

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)

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Updated by Andrea Dell'Amico about 9 years ago

Assignee changed from Andrea Dell'Amico to _InfraScience Systems Engineer

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Updated by Pasquale Pagano about 9 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.

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Updated by Andrea Dell'Amico about 9 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.

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Updated by Andrea Dell'Amico about 9 years ago

Due date set to Apr 15, 2016

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

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Updated by Gabriele Giammatteo about 9 years ago

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

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Updated by Gianpaolo Coro about 9 years ago

Parent task changed from #698 to #630

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Updated by Massimiliano Assante about 9 years ago

Tracker changed from Support to Task

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Updated by Andrea Dell'Amico about 9 years ago

Status changed from New to In Progress

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Updated by Andrea Dell'Amico about 9 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.

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#10

Updated by Andrea Dell'Amico about 9 years ago

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

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#11

Updated by Gianpaolo Coro about 9 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?

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#12