[datatable-help] fread on very large file

[Paul Harding]

Problem with fread on a large file

The file is 8GB, just short of 200,000 lines, produced as SQLoutput and
modified by cygwin/perl to remove the second line.

Using data.table 1.8.8 on R3.0.0 I get an fread error

fread("data/spd_all_fixed.csv",sep=",")
Error in fread("data/spd_all_fixed.csv", sep = ",") :
  Expected sep (',') but '0' ends field 5 on line 6 when detecting types:
204038,2617097,20110803,0,0

Looking for the offending line,with line numbers in output so I'm guessing
this is line 6 of the mid-file chunk examined,

$ grep -n '204038,2617097,201108' spd_all_fixed.csv
8316105:204038,2617097,20110801,0,0,0.64220529999999998,0,0,0
8751106:204038,2617097,20110802,1,0,0.65744469999999999,0,0,0
9186294:204038,2617097,20110803,0,0,0.49455500000000002,0,0,0
9621619:204038,2617097,20110804,0,0,0.3461342,0,0,0
10057189:204038,2617097,20110805,0,0,0.34128710000000001,0,0,0

and comparing to surrounding lines and the first ten lines

$ head  spd_all_fixed.csv
s_key,i_key,p_key,q,pq,d,l,epi,class
203974,1107181,20110713,0,0,0.13700080000000001,0,0,0
203975,1107181,20110713,0,0,5.8352899999999999E-2,0,0,0
203976,1107181,20110713,0,0,7.1298999999999998E-3,0,0,0
203978,1107181,20110713,0,0,0.78346819999999995,0,0,0
203979,1107181,20110713,0,0,0.61627779999999999,0,0,0
203981,1107181,20110713,1,0,0.38610509999999998,0,0,0
203982,1107181,20110713,0,0,4.0657899999999997E-2,0,0,0
203983,1107181,20110713,2,0,0.71278109999999995,0,0,0
203984,1107181,20110713,0,0,0.42634430000000001,0.42634430000000001,2,13

I can't see any difference. I wonder if this is a bug? I have no problems
on a small test data set run through an identical process and using the
same fread command.

Regards
Paul
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/datatable-help/attachments/20130430/f3b0001f/attachment-0001.html>