[datatable-help] Problem with data.table and FastRWeb
Matt Dowle
mdowle at mdowle.plus.com
Tue Feb 18 11:43:03 CET 2014
Hi Mel,
Thanks for the info. It's likely related to cedta() and we can handle
it from data.table's side as follows.
Background :
http://stackoverflow.com/a/10529888/403310
Type "data.table:::cedta" so you can see the rules. I guess FastWeb is
running your code in its own environment. First thing, turn on verbosity :
options(data.table.verbose=TRUE) # or for one statement rather
than globally, d1[d2,verbose=TRUE]
and run your code again. You should see a message "cedta decided
'<nsname>' wasn't data.table aware", where <nsname> is probably "FastRWeb".
This calling environment (let's assume "FastRWeb" from now on) is more
like .GlobalEnv than a package; i.e., it's where you run your own
code, you've done library(data.table) in that environment, and so it is
data.table aware as far as you're concerned. So what to do? There are
two override mechanisms :
The data.table package contains a character vector :
> data.table:::cedta.override
[1] "gWidgetsWWW"
It already contains one package which is similar in nature. You can add
FastRWeb to that vector yourself as follows :
> assignInNamespace("cedta.override", c("gWidgetsWWW","FastRWeb"),
"data.table")
> data.table:::cedta.override
[1] "gWidgetsWWW" "FastRWeb"
But I'll also add FastRWeb to that vector in data.table, so from the
next version of data.table you won't have to do it yourself. We'll add
new packages as we become aware of them.
Alternatively, the package author (Simon in this case) can provide
data.table-awareness optionally. This mechanism was added for dplyr so
it can control data.table awareness from the caller's end. That's done
by setting a variable .datatable.aware=TRUE|FALSE in the calling
package's namespace. However, in the case of FastRWeb, the
cedta.override on data.table's side seems the right way to go.
Matt
On 18/02/14 05:31, Bacou, Melanie wrote:
> Hi Arun,
>
> This is a little tricky to reproduce unless you have installed
> FastRWeb, and then started the FastRWeb server. I'm executing these
> scripts from the browser through a call to FastRWeb running on a local
> port.
>
> Installation is documented here and is quick and straightforward on Linux:
> https://rforge.net/FastRWeb/
> and an example here:
> http://jayemerson.blogspot.mx/2011/10/setting-up-fastrwebrserve-on-ubuntu.html
>
> I'm using FastRWeb to build a simple web service. As long as I stick
> to data.frame methods, everything works fine and I get the expected
> plots and HTML output in the browser. But calls to data.table methods
> (merge, extract) all seem to default to data.frame, and I really don't
> know how to debug that.
>
> I am copying Simon Urbanek who's the maintainer of FastRWeb, in case
> this is more of a FastRWeb issue.
>
> Here is my session info (I am on CentOS 5 and cannot easily upgrade to
> R 3.0.2).
>
> > sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics utils datasets grDevices methods base
>
> other attached packages:
> [1] ggmap_2.3 ggplot2_0.9.3.1 RColorBrewer_1.0-5
> raster_2.2-12
> [5] rgeos_0.3-3 rgdal_0.8-16 sp_1.0-14 data.table_1.8.10
> [9] RJDBC_0.2-3 rJava_0.9-6 DBI_0.2-7 rj_1.1.2-3
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-23 RJSONIO_1.0-3 RgoogleMaps_1.2.0.5
> [4] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4
> [7] grid_2.15.2 gtable_0.1.2 labeling_0.2
> [10] lattice_0.20-24 mapproj_1.2-2 maps_2.3-6
> [13] munsell_0.4.2 plyr_1.8 png_0.1-7
> [16] proto_0.3-10 reshape2_1.2.2 rj.gd_1.1.0-1
> [19] rjson_0.2.13 scales_0.2.3 stringr_0.6.2
> [22] tools_2.15.2
>
> Thanks all!
> --Mel.
>
>
>
>
> On 2/17/2014 6:58 AM, Arunkumar Srinivasan wrote:
>> Mel,
>> I'm not able to reproduce this on 1.8.11. Which version are you using?
>> I'm not aware of this package, and what 'otable' is supposed to do.
>> But I get no output while running your script, and not the error
>> message as well.
>>
>>
>> On Mon, Feb 17, 2014 at 11:14 AM, Bacou, Melanie <mel at mbacou.com
>> <mailto:mel at mbacou.com>> wrote:
>>
>> Hi,
>>
>> I am testing an R script using FastRWeb (through Rserve).
>> FastRWeb works as expected and I can successfully runs Simon
>> Urbanek's examples. Problems arise when I try to merge
>> datatables. It seems FastRWeb cannot find merge.data.table().
>>
>> I'm using plenty of other libraries (ggplot, raster, RJDBC, etc.)
>> that execute successfully through FastRWeb scripts, so I'm
>> guessing it's something peculiar to data.table.
>>
>> Thanks for any help! --Mel.
>>
>>
>> Here are reproducible examples.
>>
>> Test #1: the code below (the entire content of my R script) SUCCEEDS:
>>
>> # test1.R
>> library(data.table)
>>
>> run <- function(...) {
>> oclear()
>> d1 <- data.table(a=c(1,2,3), b=c("a","b","c"))
>> d2 <- data.table(e=c("v","a","b"), f=c(4,6,7))
>> otable(d1)
>> otable(d2)
>> }
>>
>> This returns a simple web page showing 2 tables:
>> 1 a
>> 2 b
>> 3 c
>>
>> v 4
>> a 6
>> b 7
>>
>>
>>
>> Test #2: the code below (the entire content of my R script) FAILS
>> with:
>> Error in `[.default`(x, i) : invalid subscript type 'list'
>>
>> # test2.R
>> library(data.table)
>>
>> run <- function(...) {
>> oclear()
>> d1 <- data.table(a=c(1,2,3), b=c("a","b","c"))
>> d2 <- data.table(e=c("v","a","b"), f=c(4,6,7))
>> otable(d1)
>> otable(d2)
>> setkey(d1, b)
>> setkey(d2, e)
>> otable(d1[d2])
>> }
>>
>>
>>
>>
>> --
>> Melanie BACOU
>> International Food Policy Research Institute
>> Agricultural Economist, HarvestChoice
>> Work+1(202)862-5699 <tel:%2B1%28202%29862-5699>
>> E-mailmel at mbacou.com <mailto:mel at mbacou.com>
>> Visitharvestchoice.org <http://harvestchoice.org>
>>
>>
>> _______________________________________________
>> datatable-help mailing list
>> datatable-help at lists.r-forge.r-project.org
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>>
>>
>
> --
> Melanie BACOU
> International Food Policy Research Institute
> Agricultural Economist, HarvestChoice
> Work +1(202)862-5699
> E-mailmel at mbacou.com
> Visit harvestchoice.org
>
>
> _______________________________________________
> datatable-help mailing list
> datatable-help at lists.r-forge.r-project.org
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