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Segfault with fread #2299

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etienne-s opened this issue Aug 14, 2017 · 1 comment
Closed

Segfault with fread #2299

etienne-s opened this issue Aug 14, 2017 · 1 comment

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@etienne-s
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etienne-s commented Aug 14, 2017

I get a segfault when using fread on this file: test.txt

I use the latest dev version, the problem does not occur with the CRAN version.

The file can be fixed by adding a separator at the end of line 116.

Not sure whether it is related to an existing issue or not.

@st-pasha st-pasha added the fread label Aug 14, 2017
@st-pasha
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st-pasha commented Aug 14, 2017

On my MacOS machine, I get the following:

> fread("~/Downloads/test.txt")
Error in fread("~/Downloads/test.txt") : 
  Expecting 7 cols but row 0 contains only 6 cols (sep='|'). Consider fill=true. <<"aa aa aa aa aa aa aa aa !"|1|aa.aa.aa|"aa aa aa aa aa aa aa aa ! 1 aaûaa 1 aa aa1 aa : aa aa aa'aa aa aa aaé aa aa aa aa ! aa aa aa aa !"|aa aa aa aa aa aa aa aa ! ,|>>

This is a valid error message (except that the line number is incorrect) -- the line shown does have 6 fields instead of expected 7; and adding option fill=TRUE does read the file correctly. There is no segfault.


On a Windows machine however, I can confirm that running fread("test.txt") produces a segfault, whereas fread("test.txt", fill=T) reads the data correctly. Here's the log leading up to the segfault:

> fread("Downloads/test.txt", verbose=T)
Input contains no \n. Taking this to be a filename to open
[1] Check arguments
  Using 8 threads (omp_get_max_threads()=8, nth=8)
  NAstrings = [<<NA>>]
  None of the NAstrings look like numbers.
  show progress = 1
[2] Opening the file
  Opening file Downloads/test.txt
  File opened, size = 95.7KB (zd bytes).
  Memory mapping ... ok
[3] Detect and skip BOM
[4] Detect end-of-line character(s)
  Detected eol as \r\n (CRLF) in that order, the Windows standard.
[6] Skipping initial rows if needed
  Positioned on line 1 starting: <<aa|aa aa|aa|aa|aa|aa aa|aa aa>>
[7] Detect separator, quoting rule, and ncolumns
  Detecting sep ...
  sep=','  with 1 lines of 3 fields using quote rule 2
  sep='|'  with 100 lines of 7 fields using quote rule 0
  Detected 7 columns on line 1. This line is either column names or first data row. Line starts as: <<aa|aa aa|aa|aa|aa|aa aa|aa aa>>
  Quote rule picked = 0
[8] Determine column names
  All the fields on line 1 are character fields. Treating as the column names.
[9] Detect column types
  Number of sampling jump points = 11 because (97943 bytes from row 1 to eof) / (2 * 4859 jump0size) == 10
  Type codes (jump 000)    : 6266622  Quote rule 0
Bumping quote rule from 0 to 1 due to field 1 on line 7 of sampling jump 1 starting <<"aa : aaAcaa aa aa aa aa aa "aa aa aa" ?"|1|aa-aa.aa|"-"|||>>
Bumping quote rule from 1 to 2 due to field 1 on line 7 of sampling jump 1 starting <<"aa : aaAcaa aa aa aa aa aa "aa aa aa" ?"|1|aa-aa.aa|"-"|||>>
  Type codes (jump 001)    : 6266622  Quote rule 2
  Type codes (jump 010)    : 6266622  Quote rule 2
  =====
  Sampled 1039 rows (handled \n inside quoted fields) at 11 jump points
  Bytes from first data row on line 2 to the end of last row: 97943
  Line length: mean=61.00 sd=19.55 min=22 max=146
  Estimated number of rows: 97943 / 61.00 = 1606
  Initial alloc = 3212 rows (1606 + 100%) using bytes/max(mean-2*sd,min) clamped between [1.1*estn, 2.0*estn]
  =====
[10] Apply user overrides on column types
After 0 type and 0 drop user overrides : 6266622
[11] Allocate memory for the datatable
  Allocating 7 column slots (7 - 0 dropped) with 3212 rows
[12] Read the data

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