(question is not relevant anymore, since new version of data.table of 25-NOV-2016 - see accepted answer below)
So, I have a table with some empty lines
Version 1.9.8 of data.table, released 25-NOV-2016, has a new blank.lines.skip option to skip blank lines.
text <- "1,a\n\n2,b\n3,c\n4,a\n\n5,b\n\n6,c"
library(data.table)
fread(text)
## V1 V2
## 1: 2 b
## 2: 3 c
## 3: 4 a
## Warning message:
## In fread("1,a\n\n2,b\n3,c\n4,a\n\n5,b\n\n6,c") :
## Stopped reading at empty line 6 but text exists afterwards (discarded): 5,b
fread(text, blank.lines.skip=TRUE)
## V1 V2
## 1: 1 a
## 2: 2 b
## 3: 3 c
## 4: 4 a
## 5: 5 b
## 6: 6 c