R devel - Aug 2008 - scan after seek in text files (PR#12640)

Full_Name: Dr. Alex Sheppard
Version: 2.7.1
OS: Linux Debian Lenny
Submission from: (NULL) (79.73.224.62)


After scanning from an open (text) connection, then seeking, then scanning
again, the second scan returns incorrect result. It looks like the first byte
scanned was from the pre-seek file position, then it continues to read from the
post-seek file position. 


To reproduce:

#Put 3x3 matrix in a file
>
write.matrix(t(matrix(1:9,nrow=3)),file="TEST.txt",sep="\t")
#Open file as text
> fd <- file("TEST.txt",open="rt")
#scan a couple of fields - this looks fine so far
> scan(file=fd,what=double(),n=2)
Read 2 items
[1] 1 2

#seek back to start of file
> seek(con=fd,where=0,origin="start")
[1] 5

#scan fields again - this doesn't work properly
> scan(file=fd,what=double(),n=2)
Read 2 items
[1] 31  2

This happens when either n or nmax arguments are used to control number of
fields read. Problem does not occur when using nlines argument instead. The seek
appears to work ok, as doing readChar(fd,n=1) after the seek operation correctly
returns "1". 
Also, if the file is opened as binary, i.e.
fd=file("TEST.txt",open="rb") , all
works fine.

The issue is the pushback on text files (which readChar does not use).
I've altered the logic in 2.7.2 patched so that seek() clears the 
pushback.

NB:
1) Your code is incomplete (you need library(MASS)),
2) You are asked not to report on obsolete versions of R.

On Sat, 30 Aug 2008, alex at apeironsports.com wrote:
> Full_Name: Dr. Alex Sheppard
> Version: 2.7.1
> OS: Linux Debian Lenny
> Submission from: (NULL) (79.73.224.62)
>
>
> After scanning from an open (text) connection, then seeking, then scanning
> again, the second scan returns incorrect result. It looks like the first
byte
> scanned was from the pre-seek file position, then it continues to read from
the
> post-seek file position.
>
>
> To reproduce:
>
> #Put 3x3 matrix in a file
>>
write.matrix(t(matrix(1:9,nrow=3)),file="TEST.txt",sep="\t")
>
> #Open file as text
>> fd <- file("TEST.txt",open="rt")
>
> #scan a couple of fields - this looks fine so far
>> scan(file=fd,what=double(),n=2)
> Read 2 items
> [1] 1 2
>
> #seek back to start of file
>> seek(con=fd,where=0,origin="start")
> [1] 5
>
> #scan fields again - this doesn't work properly
>> scan(file=fd,what=double(),n=2)
> Read 2 items
> [1] 31  2
>
> This happens when either n or nmax arguments are used to control number of
> fields read. Problem does not occur when using nlines argument instead. The
seek
> appears to work ok, as doing readChar(fd,n=1) after the seek operation
correctly
> returns "1".
> Also, if the file is opened as binary, i.e.
fd=file("TEST.txt",open="rb") , all
> works fine.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595