[datatable-help] Memory issue
Gene Leynes
gleynes+r at gmail.com
Tue Oct 23 16:56:19 CEST 2012
Judging from the unusual silence I'm guessing that this doesn't have an
obvious solution. I can't provide the data, and in my simulated data I
don't get the same error.
I'll do some more testing today and see if I can isolate the problem.
I have a suspicion about the cause, and ill teat that. The problem seems
related to one particularly messy text field. I will bet that there is some
combination of characters that is causing the problem. Or some of them are
too long.
I could split the file and see if each part blows up in size when I save,
in order to isolate the problem.
Thanks, and my apologies for being unable to send a good example.
On Thursday, October 18, 2012, Gene Leynes wrote:
> Ok, here is my very lengthy reply with lots of diagnostics.
>
>
> >
> > ## Clear the workspace
> > rm(list=ls())
> >
> > ## I use a function called "loader" to load single data objects
> > if(!require('geneorama')){
> + source('https://raw.github.com/geneorama/geneorama/master/R/loader.R')
> + cat('loading function \"loader\"')
> + }
> >
> > ## Load the data
> > Small = loader('test0')
> > Large = loader('test1')
> >
> > ## The two files will be different because their order is different
> > str(Small)
> Classes ‘data.table’ and 'data.frame': 3103314 obs. of 42 variables:
> $ index : int 1 2 3 4 5 6 7 8 9 10 ...
> $ char1 : chr "http://conradhotels3.hilton.com" "
> http://conradhotels3.hilton.com" "http://conradhotels3.hilton.com" "
> http://conradhotels3.hilton.com" ...
> $ char2 : chr "/en/index.html" "/en/index.html" "/en/index.html"
> "/en/index.html" ...
> $ char3 : chr "" "" "" "" ...
> $ int1 : int 44903 44903 44903 44903 44903 44903 44903 44903 44903
> 44903 ...
> $ int2 : int 411 411 254 254 336 336 118 118 386 386 ...
> $ char4 : chr "2012-05-09 20:17:40.587" "2012-05-09 21:17:54.427"
> "2012-05-09 20:10:49.560" "2012-05-09 21:11:05.107" ...
> $ int3 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int4 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int5 : int 69 69 69 69 69 69 69 68 68 68 ...
> $ int6 : int 68 68 68 68 68 68 68 67 67 67 ...
> $ int7 : int 35 35 37 35 35 35 33 38 38 40 ...
> $ int8 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int9 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int10 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int11 : int 1 1 1 1 1 1 1 1 1 1 ...
> $ int12 : int 334830 334847 335102 334838 334836 342687 334521 318626
> 318578 326800 ...
> $ int13 : int 36 36 37 36 36 36 35 38 37 39 ...
> $ int14 : int 44 44 49 47 45 45 45 46 45 48 ...
> $ char5 : chr "" "" "" "" ...
> $ int15 : int NA NA NA NA NA NA NA NA NA NA ...
> $ int16 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int17 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int18 : int 2 2 2 2 2 2 2 2 2 2 ...
> $ int19 : int 1381 1152 424 3728 1772 921 385 725 401 314 ...
> $ int20 : int 36 36 37 36 36 36 35 38 37 39 ...
> $ int21 : int 2199 2201 1492 1448 2559 2529 1084 1432 1876 1984 ...
> $ int22 : int 44 44 49 47 45 45 45 46 45 48 ...
> $ int23 : int 2203 2188 1199 1162 2324 2346 821 897 1386 1189 ...
> $ int24 : int 13 13 14 13 13 13 12 13 13 14 ...
> $ int25 : int 5166 5761 3755 3794 5614 7779 2830 3971 4637 5871 ...
> $ int26 : int 103 103 105 103 103 103 101 105 105 107 ...
> $ int27 : int 70 183 159 197 217 165 153 232 92 102 ...
> $ int28 : int 103 103 105 103 103 103 101 105 105 107 ...
> $ int29 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int30 : int 161 146 200 158 150 160 190 161 163 169 ...
> $ char6 : chr "Limelight" "Limelight" "Fusepoint/Savvis"
> "Fusepoint/Savvis" ...
> $ char7 : chr "Paris" "Paris" "Toronto" "Toronto" ...
> $ char8 : chr "-1" "-1" "-1" "-1" ...
> $ char9 : chr "FRANCE" "FRANCE" "CANADA" "CANADA" ...
> $ char10: chr "FR" "FR" "CA" "CA" ...
> > str(Large)
> Classes ‘data.table’ and 'data.frame': 3103314 obs. of 42 variables:
> $ index : int 716234 716235 1007651 2679944 1550732 1932010 2879445
> 1007670 1736006 666363 ...
> $ char1 : chr "http://go.compuware.com" "http://go.compuware.com" "
> http://www.achmeacollectief.nl" "https://db3.notify.windows.com" ...
> $ char2 : chr "/default.aspx" "/dynaTraceMonitor" "/unilever/" "/ping"
> ...
> $ char3 : chr "?rurl=
> http://frontline.compuware.com//products/BU/default.aspx"
> "?url=http%3A%2F%2Fgo.compuware.com%2Fdefault.aspx%3Frurl%3Dhttp%3A%2F%
> 2Ffrontline.compuware.com%2F%2Fproducts%2FBU%2Fdefault.as"| __truncated__
> "" "" ...
> $ int1 : int 2812881 2812881 3149757 4286896 3618836 3861870 4315803
> 3149760 3779387 2754629 ...
> $ int2 : int 133 133 133 133 340 340 326 133 133 340 ...
> $ char4 : chr "2012-05-09 20:00:00.000" "2012-05-09 20:00:00.000"
> "2012-05-09 20:00:00.000" "2012-05-09 20:00:00.000" ...
> $ int3 : int 0 1 0 0 0 0 0 0 0 0 ...
> $ int4 : int 2264 2496 1782 461 1953 1418 641 1207 167 278 ...
> $ int5 : int 26 20 6 1 71 64 1 6 1 15 ...
> $ int6 : int 26 20 6 1 69 64 1 6 1 15 ...
> $ int7 : int 2 2 4 0 2 12 0 2 0 0 ...
> $ int8 : int 0 0 0 0 2 0 0 0 0 0 ...
> $ int9 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int10 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int11 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int12 : int 392752 417195 43107 0 1419015 1031349 187344 62969 43
> 428189 ...
> $ int13 : int 4 4 5 1 8 22 1 3 1 1 ...
> $ int14 : int 9 11 8 1 17 38 1 6 1 15 ...
> $ char5 : chr "" "" "" "" ...
> $ int15 : int NA NA NA NA 0 NA NA NA NA 0 ...
> $ int16 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int17 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int18 : int 2 28 3 0 0 1 0 1 0 0 ...
> $ int19 : int 137 0 136 298 277 255 147 141 137 209 ...
> $ int20 : int 4 0 5 1 8 22 1 3 1 1 ...
> $ int21 : int 945 612 59 22 689 1153 54 29 13 59 ...
> $ int22 : int 9 5 8 1 17 38 1 6 1 15 ...
> $ int23 : int 0 0 0 118 0 0 0 0 0 0 ...
> $ int24 : int 0 0 0 1 0 0 0 0 0 0 ...
> $ int25 : int 3243 2653 1585 22 3292 3076 64 1043 13 81 ...
> $ int26 : int 28 22 10 1 73 76 1 8 1 15 ...
> $ int27 : int 2060 3365 257 1 3304 1038 376 258 4 80 ...
> $ int28 : int 28 22 10 1 73 76 1 8 1 15 ...
> $ int29 : int 0 0 0 0 0 0 0 0 0 0 ...
> $ int30 : int 921 750 203 578 609 1078 234 187 31 140 ...
> $ char6 : chr "Interoute" "Interoute" "Interoute" "Interoute" ...
> $ char7 : chr "Amsterdam" "Amsterdam" "Amsterdam" "Amsterdam" ...
> $ char8 : chr "-1" "-1" "-1" "-1" ...
> $ char9 : chr "NETHERLANDS" "NETHERLANDS" "NETHERLANDS" "NETHERLANDS" ...
> $ char10: chr "NL" "NL" "NL" "NL" ...
> $ char11: chr "NETHERLANDS" "NETHERLANDS" "NETHERLANDS" "NETHERLANDS" ...
> - attr(*, ".internal.selfref")=<externalptr>
> - attr(*, "sorted")= chr "char4"
> >
> > ## The difference is shown here
> > mapply(identical, Small, Large)
> index char1 char2 char3 int1 int2 char4 int3 int4 int5
> int6 int7 int8 int9
> FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
> FALSE FALSE FALSE FALSE
> int10 int11 int12 int13 int14 char5 int15 int16 int17 int18
> int19 int20 int21 int22
> FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
> FALSE FALSE FALSE FALSE
> int23 int24 int25 int26 int27 int28 int29 int30 char6 char7
> char8 char9 char10 char11
> FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
> FALSE FALSE FALSE FALSE
> > mapply(all.equal, Small, Large)
> index
> "Mean relative difference: 0.6660698"
> char1
> "3100674 string mismatches"
> char2
> "2961621 string mismatches"
> char3
> "1753352 string mismatches"
> int1
> "Mean relative difference: 0.2945024"
> int2
> "Mean relative difference: 0.4866954"
> char4
> "3103308 string mismatches"
> int3
> "Mean relative difference: 1.759713"
> int4
> "Mean relative difference: 1.408616"
> int5
> "Mean relative difference: 1.411817"
> int6
> "Mean relative difference: 1.415648"
> int7
> "Mean relative difference: 1.705137"
> int8
> "Mean relative difference: 1.954795"
> int9
> "Mean relative difference: 1.99701"
> int10
> "Mean relative difference: 1.995529"
> int11
> "Mean relative difference: 2"
> int12
> "Mean relative difference: 1.479043"
> int13
> "Mean relative difference: 1.323619"
> int14
> "Mean relative difference: 1.360022"
> char5
> "1454309 string mismatches"
> int15
> "'is.NA' value mismatch: 2260789 in current 2260789 in target"
> int16
> "Mean relative difference: 1.997195"
> int17
> "Mean relative difference: 2"
> int18
> "Mean relative difference: 1.799441"
> int19
>
>
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