[datatable-help] fread crashes reading R when reading csv

[Ben Weinstein]

Data table crashes

I am having a similar issue to this post:
http://r.789695.n4.nabble.com/fread-crash-td4683394.html

please see markdown script: http://rpubs.com/bw4sz0511/16766 or text below:
or text below:

The file is about 550MB, i'm unsure how many rows it actually is (several
million).

When i try to run fread, Rstudio just crashes with no error. I can read in
up to about 15 rows


require(data.table)
## Loading required package: data.table

# env dist table

env <- fread("EnvData.csv", nrows = 15, verbose = TRUE)
## Input contains no \n. Taking this to be a filename to open
## File opened, filesize is  0.543B
## File is opened and mapped ok
## 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 4 columns
## First row with 4 fields occurs on line 2 (either column names or first
row of data)
## Some fields on line 2 are not type character (or are empty). Treating as
a data row and using default column names.
## Count of eol after first data row: 15989212
## Subtracted 0 for last eol and any trailing empty lines, leaving 15989212
data rows
## nrow limited to nrows passed in (15)
## Type codes: 4113 (first 5 rows)
## Type codes: 4113 (after applying colClasses and integer64)
## Type codes: 4113 (after applying drop or select (if supplied)
## Allocating 4 column slots (4 - 0 NULL)
##    0.000s (  0%) Memory map (rerun may be quicker)
##    0.000s (  0%) sep and header detection
##    0.702s (100%) Count rows (wc -l)
##    0.000s (  0%) Column type detection (first, middle and last 5 rows)
##    0.000s (  0%) Allocation of 15x4 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
##    0.702s        Total

head(env)
##    V1 V2 V3     V4
## 1:  1  2  1  249.3
## 2:  2  3  1  536.9
## 3:  3  4  1 1161.8
## 4:  4  5  1 1234.0
## 5:  5  6  1 1513.4
## 6:  6  7  1 1757.1
However when i run fread with more than 20 rows, it crashes Rstudio.

# not run
env <- fread("EnvData.csv", nrows = 25, verbose = TRUE)
verbose on the error output reads:

Input contains no \n. Taking this to be a filename to open

File opened, filesize is 0.543B

File is opened and mapped ok

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 4 columns

First row with 4 fields occurs on line 2 (either column names or first row
of data)

Some fields on line 2 are not type character (or are empty). Treating as a
data row and using default column names.

Count of eol after first data row: 15989212

Subtracted 0 for last eol and any trailing empty lines, leaving 15989212
data rows

nrow limited to nrows passed in (25)

Type codes: 4113 (first 5 rows)

Type codes: 4113 (+middle 5 rows)

Look at the file, nothing seems wrong


env <- read.csv("EnvData.csv", nrows = 25)

env
##    V1 V2     V3
## 1   2  1  249.3
## 2   3  1  536.9
## 3   4  1 1161.8
## 4   5  1 1234.0
## 5   6  1 1513.4
## 6   7  1 1757.1
## 7   8  1 2176.7
## 8   9  1 2644.0
## 9  10  1 3033.3
## 10 11  1 3721.2
## 11 12  1 4432.8
## 12 13  1 4609.6
## 13 14  1 5378.8
## 14 15  1 5953.6
## 15 16  1 5913.9
## 16 17  1 6281.3
## 17 18  1 6669.7
## 18 19  1 6449.7
## 19 20  1 6218.4
## 20 21  1 6493.4
## 21 22  1 6056.6
## 22 23  1 5275.8
## 23 24  1 4605.2
## 24 25  1 3153.9
## 25 26  1 2532.1


Thanks for your help,

Ben Weinstein
-- 
Ben Weinstein
PhD Candidate
Ecology and Evolution
Stony Brook University

http://benweinstein.weebly.com/
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