Read space delimited file where missing values are blank "".

Start by reproducing the issue with fread("fileTest.txt", strip.white = FALSE) using the three-row example and compare the behavior described for data.table 1.10.4 and 1.12.2. Done means space-delimited blank fields are retained as missing values rather than causing an early stop, with regression coverage added for this input.

Example input text file - fileTest.txt:

c1 c2 c3 c4 c5 c6
r1 0 1 2 3 4
r2 0   3 4
r3 0 1 2 3 4

Adding a screenshot to show there are 3 spaces on row r2 between 0 and 3, i.e.: values are missing for c3 and c4.

Using R version 3.4.0 and data.table 1.10.4 (Session info 1), below works as expected:

> fread("fileTest.txt", strip.white = FALSE)
   c1 c2 c3 c4 c5 c6
1: r1  0  1  2  3  4
2: r2  0 NA NA  3  4
3: r3  0  1  2  3  4

But fails with R version 3.5.2 and data.table_1.12.2. (Session info 2).

> fread("fileTest.txt", strip.white = FALSE)
   c1 c2 c3 c4 c5 c6
1: r1  0  1  2  3  4
Warning message:
In fread("fileTest.txt", strip.white = FALSE) :
  Stopped early on line 3. Expected 6 fields but found 4. Consider fill=TRUE and comment.char=. First discarded non-empty line: <<r2 0   3 4>>

Other attempts, all failed:

fread("fileTest.txt")
fread("fileTest.txt", sep = " ")
fread("fileTest.txt", strip.white = FALSE)
fread("fileTest.txt", sep = " ", strip.white = FALSE, na.strings = c("NA", ""))
fread("fileTest.txt", sep = " ", strip.white = FALSE, quote = "")

Note

• I checked the NEWs, SO, Google, couldn't find anything easily relevant info.
• Related SO post: How to read when delimiter is space and missing values are blank?
• read.table works as expected, but my files are huge (millions of rows), hence trying to use fread:

read.table("fileTest.txt", strip.white = FALSE, sep = " ", na.strings = "")

Session info 1

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /opt/gridware/apps/intel/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] data.table_1.10.4

loaded via a namespace (and not attached):
[1] compiler_3.4.0

Session info 2

R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] data.table_1.12.2

loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2