[datatable-help] dancing with alloc.col

Kaupas, George George.Kaupas at spansion.com
Wed Aug 8 20:17:39 CEST 2012

Thanks for the quick and patient response, as it was indeed my own fault.

In the interest of debugging I had set options(warn=3) as well as options(datatable.verbose=TRUE); setting warn=0 does indeed allow my code to run to satisfactory completion.

I have to stop ignoring the subtle (to me) messages R throws; in this case, "Error in ... (converted from warning)".

So a followup general R question is, if I use options(warn=0), my .Rout contains a line like "There were 46 warnings (use warnings() to see them)". If instead I wrap the := statements with suppressWarnings(), I don't get that. Is there a way to suppress the "There were n warnings" message?

-----Original Message-----
From: Matthew Dowle [mailto:mdowle at mdowle.plus.com] 
Sent: Wednesday, August 08, 2012 5:45 AM
To: Kaupas, George
Cc: datatable-help at lists.r-forge.r-project.org
Subject: Re: [datatable-help] dancing with alloc.col

Oh and since you're looping the := or set(), then options(warn=0) before the loop is probably faster than repeated calls to suppressWarnings().

> :)
> When the column allocation is full, there's a formula to decide how 
> much to grow the allocation by. The check is there (iirc) to make sure 
> that's not growing the table too much. If you have 1 million columns, 
> you probably don't want to double that to 2 million, just to add 1 
> column. But if you do, then use alloc.col first. That was the 
> thinking. But that thinking is biting in your case.
> Simplest might be to downgrade the warning to a message when verbosity 
> is on, then.
> In the meantime, does wrapping with suppressWarning() work around it 
> for now? Since in your case you know that over-allocating by more than 
> 1000 is appropriate.
>     suppressWarnings(DT[,newcol:=])
> Thanks for reporting. Interesting use case.
> Matthew
>> I'm running into this "truelength is greater than 1000 items 
>> over-allocated" warning/error as I use := to add columns to a 
>> data.frame,
>> e.g.:
>> tl (1346) is greater than 1000 items over-allocated (ncol = 308). If 
>> you didn't set the datatable.alloccol option very large, please 
>> report this to datatable-help including the result of sessionInfo().
>> The long preamble to this is a stackoverflow thread
>> (http://stackoverflow.com/questions/10015544) in which I needed to 
>> update the contents of one data.table with the contents of another.
>> The solution required the columns of both data.tables to match, hence 
>> my pre-processing loop to add columns to each data.table to satisfy 
>> the
>> identical(names(dt1),names(dt2)) criteria. I may have to re-architect 
>> this depending on what is going on with this allocation business.
>> If, for example, dt1 has 200 columns, and dt2 has 2000, and together 
>> they have 2100 unique columns, I'm going to add 1900 columns to dt1. 
>> If I set alloc.col to 2100 before my column-adding loop, I'll get 
>> slapped because
>> 2100 is more than 1000 greater than the 200 columns present in dt1.
>> So do I need to spoon-feed alloc.col? Every iteration through the 
>> loop set it to length(dt1)+1 before adding a column? That seems 
>> rather brutal.
>> Alternatively checking for the delta between truelength and length, 
>> and how close that is to the magic 1000 number, and then only 
>> adjusting the setting seems fragile.
>> I did try to make sense of the help for alloc.col. Regarding the bit 
>> about "if two or more variables are bound to the same data.table"; 
>> the column addition is within a function, and only one variable 
>> references the data.table, at least in the scope of the function. The 
>> function calling that function has a variable for the data.table too, 
>> so I don't know if that counts. Then there is mention of using copy 
>> (not sure how that helps, and BTW the hyperlink for copy goes to the 
>> page for setkey, which does mention copy, but suggests "See ?copy" 
>> which just conjures up the setkey page again), setting alloc.col, or 
>> changing datatable.alloccol (doesn't seem to help).
>> The warning asked for sessionInfo; FWIW, here it is:
>> R version 2.15.0 (2012-03-30)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>> [7] LC_PAPER=C                 LC_NAME=C
>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods
>> [7] base
>> other attached packages:
>> [1] data.table_1.8.2
>> Thanks
>> George
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