[datatable-help] fread crash

[Matt Dowle]

On 10/01/14 16:04, statquant3 wrote:
> R) sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> locale:
> [1] C
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
> other attached packages:
> [1] data.table_1.8.11 [**something I cannot disclose (...I know...)**]
> loaded via a namespace (and not attached):
> [1] plyr_1.8       reshape2_1.2.2 stringr_0.6.2
>
> ======================================================
> R) data <- fread(FILE, verbose=T)
> Input contains no \n. Taking this to be a filename to open
> Detected eol as \n only (no \r afterwards), the UNIX and Mac standard.
> Using line 30 to detect sep (the last non blank line in the first
> 'autostart') ... sep=','
> Found 22 columns
> First row with 22 fields occurs on line 1 (either column names or first row
> of data)
> All the fields on line 1 are character fields. Treating as the column names.
> Count of eol after first data row: 5094763
> Subtracted 0 for last eol and any trailing empty lines, leaving 5094763 data
> rows
> Type codes: 4444444433333331411433 (first 5 rows)
> Type codes: 4444444433333333431433 (+middle 5 rows)

Seems to be crashing when detecting types using the last 5 rows. Can you 
say anything odd near the end of the file?
>
>   *** caught segfault *** address 0x2ae7f1a000, cause 'memory not mapped'
>
> Traceback:
>   1: fread(FILE, verbose = T)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> ====================
> Here is the output for 5 lines, it worked this time
>
> R) dataT <- fread(FILE, nrow=5, verbose=T)
> Input contains no \n. Taking this to be a filename to open
> Detected eol as \n only (no \r afterwards), the UNIX and Mac standard.
> Using line 30 to detect sep (the last non blank line in the first
> 'autostart') ... sep=','
> Found 22 columns
> First row with 22 fields occurs on line 1 (either column names or first row
> of data)
> All the fields on line 1 are character fields. Treating as the column names.
> Count of eol after first data row: 5094763
> Subtracted 0 for last eol and any trailing empty lines, leaving 5094763 data
> rows
> nrow limited to nrows passed in (5)
> Type codes: 4444444433333331411433 (first 5 rows)
> Type codes: 4444444433333331411433 (after applying colClasses and integer64)
> Type codes: 4444444433333331411433 (after applying drop or select (if
> supplied)
> Allocating 22 column slots (22 - 0 NULL)
>     0.000s (  0%) Memory map (rerun may be quicker)
>     0.000s (  0%) sep and header detection
>     2.760s (100%) Count rows (wc -l)
>     0.000s (  0%) Column type detection (first, middle and last 5 rows)
>     0.000s (  0%) Allocation of 5x22 result (xMB) in RAM
>     0.000s (  0%) Reading data
>     0.000s (  0%) Allocation for type bumps (if any), including gc time if
> triggered
>     0.000s (  0%) Coercing data already read in type bumps (if any)
>     0.000s (  0%) Changing na.strings to NA
>     2.760s        Total
> Warning message:
> In fread(FILE, nrow = 5, verbose = T) : Mapped file ok but madvise failed
>
>
>
>
>
> --
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