Scidbconnect() Connection error


#1

Hello, I’ve loaded the scidb library into R:

library(scidb)

and when i try to connect with a SciDB instance:

scidbconnect()

i get the following error:

scidbconnect()
Error in value[3L] : Connection error

Any suggestions on why this is happening?
Thanks,
Lily


#2

Hi,

Is SciDB running and can you connect by other means, i.e. with iquery?
Is shim running and are you able to access shim on port 8080?


#3

getting the same error, something really broken in R scidb library
scidb and shim are both running
i can connect with python to scidb and run queries no problem


#4

i have installed the latest scidbR from github ver2.0.0 and build it with R CMD build SciDBR


#5

i can connect with iquery no prob


#6

i can even submit queries via web browser and i can connect to http://localhost:8080


#7

Same issue here:

Server SciDB 15.12 & Shim 15.12 running on Ubuntu 14.04
Client SciDBR Version: 2.0.0 Date: 2015-09-07 running R version 3.3.1 (2016-06-21) running on Ubuntu 16.04

Cheers!


#9

Sorry for my last response - spoke too soon.

Try this:

options(scidb.debug=TRUE)
scidbconnect()

What does that say?


#10

Hey! - Now it says

``

library(scidb)
Attaching package: ‘scidb’
The following objects are masked from ‘package:stats’:
phyper, qhyper, reshape
The following object is masked from ‘package:base’:
substitute
options(scidb.debug=TRUE)
scidbconnect()
setopt(‘precision’,‘16’)
Error in scidbquery(query = “setopt(‘precision’,‘16’)”, release = 1, resp = TRUE) :
UserQueryException in file: src/query/OperatorLibrary.cpp function: createLogicalOperator line: 86
Error id: scidb::SCIDB_SE_QPROC::SCIDB_LE_LOGICAL_OP_DOESNT_EXIST
Error description: Query processor error. SystemException in file: src/query/OperatorLibrary.cpp function: createLogicalOperator line: 86
Error id: scidb::SCIDB_SE_QPROC::SCIDB_LE_LOGICAL_OP_DOESNT_EXIST
Error description: Query processor error. Logical operator ‘setopt’ does not exist…
setopt(‘precision’,‘16’)
^^^^^^^^^^^^^^^^^^^^^^^^


#11

Ah yes - this was fixed in the more recent version of the R package. Just re-install the latest R package from GitHub for now.


#12

It’s working now - thanks!


#14

Even after
options(scidb.debug=TRUE)
I am getting:
Error in value[3L] : Connection error

I can use iquery via the terminal. If I start R via terminal and then attempt to connect to scidb, it says:
Error in curl_fetch_memory(uri,h) : Couldn’t connect to server


#15

Do you have shim running? Can you navigate your browser to localhost:8080 and see the shim splash page?

You might also need the accelerated_io_tools library installed.


#16

I got the shim connected via the terminal by sudo service shimsvc start.
and I also executed the queries mentioned on the shim help section:

Obtain a shim session ID

id = httr::GET(“http://localhost:8080/new_session”)
session = rawToChar(id$content)

Construct the query request

query = sprintf(“http://localhost:8080/execute_query?id=%s&query=consume(list())&release=1”,
session)
ans = httr::GET(query)

The response in this example is just the SciDB query ID:

(rawToChar(ans$content)

and got the correct output as mentioned:
[1] “1457470272484488051”

but still when I execute the command
options(scidb.debug=TRUE)
scidbconnect()

output is:
options(scidb.debug=TRUE)

scidbconnect()
setopt(‘precision’,‘16’)
Error in value[3L] : Connection error


#17

That seems like a similar error to the above. The latest version of the R package should no longer call “setopt”. Try to reinstall the R package from github?

$ sudo su -
$ R
> remove.packages('scidb')
> devtools::install_github('paradigm4/SciDBR')