Error during query parsing


#1

I cannot reference arrays using scidb using the SciDB-R package.
Scidb library loads. I can connect to the scidb server and perform things like scidblist() to see what arrays are in the database.

From the vignette documentation

[code]> # Upload the Michelson-Morley experiment data to SciDB,

returning a scidbdf data frame-like object:

X <- as.scidb(morley, name=“morely”)
str(X)
Error in scidbquery(query, afl, async = FALSE, save = “lcsv+”, release = 0, :
HTTP/1.0 500 ERROR
Content-Length: 294
Content-Type: text/html

UserQueryException in file: src/query/parser/Driver.cpp function: fail line: 102
Error id: scidb::SCIDB_SE_PARSER::SCIDB_LE_QUERY_PARSING_ERROR
Error description: Error during query parsing. Query parser failed with error ‘syntax error’.
morley as array
^^^
Failed query id: 1100913112293[/code]

After that fails if you do a scidblist() you can see that the morley array was created in SciDB.
I’ve already re-installed the latest scidb-R package from github as well as reinstall shim.
I’m running 14.2 Enterprise Edition.

Doing a list('libraries) yields:

> iquery(afl=TRUE,return=TRUE,query="list('libraries')") inst n name major minor patch build build_type 1 0 0 SciDB 14 2 0 7124 RelWithDebInfo 2 0 1 libdense_linear_algebra.so 14 2 0 7124 <NA> 3 0 2 libexample_udos.so 14 2 0 7124 <NA> 4 0 3 liblinear_algebra.so 14 2 0 1514 <NA> 5 1 0 SciDB 14 2 0 7124 RelWithDebInfo 6 1 1 libdense_linear_algebra.so 14 2 0 7124 <NA> 7 1 2 libexample_udos.so 14 2 0 7124 <NA> 8 1 3 liblinear_algebra.so 14 2 0 1514 <NA>

Any ideas on what could be the problem?


#2

I can’t replicate this error, but it might be related to 14.2, which is not supported by the R package or shim.

I’ll work on building support for this as soon as possible.

–Bryan


#3

May I ask, did you build and install the shim from source?


#4

OK, sorry about that. There were recent changes to SciDB 14.x that broke the R package, but they are fixed in the latest version on Github version. Install from R with:

library(“devtools”)
install.packages(“SciDBR”,“Paradigm4”,quick=TRUE)

Things should be working for you after this update.

The official 14.3 release is coming out in a few weeks, it will be an important upgrade to SciDB.

Best,

Bryan


#5

Installed the latest version using install_github. Now I can reference SciDB matrices however when trying to view a heatmap of the matrix I am getting the following error “could not find function ‘scidb_coordinate_length’”

Error replicated using the heatmap example in the SciDBR documentation from github

[code]> iquery(“store(build(<v:double>[i=0:999,100,0,j=0:999,250,0],random()%100),A)”)

A <- scidb(“A”)
str(A)
SciDB expression: A
SciDB schema: <v:double> [i=0:999,100,0,j=0:999,250,0]

Attributes:
attribute type nullable
1 v double FALSE
Dimensions:
dimension start end chunk
1 i 0 999 100
2 j 0 999 250

X <- image(A,grid=c(100,100),op=“avg(v)”,userRaster=TRUE)
Error in .local(x, …) :
could not find function “scidb_coordinate_length”[/code]


#6

This was fixed in github commit f211328dc2d697c21e29036c33486d9caff621ca at github.com/Paradigm4/SciDBR. Sorry about that, a stupid bug on my part. I added a new test to catch this error.