Hi,
I'm running into more issues when reading data from a gzfile connection.
If I read the data sequentially with successive calls to readBin(), the
data I get looks ok. But if I call seek() between the successive calls
to readBin(), I get corrupted data.
Here is a (hopefully) reproducible example. See my sessionInfo() at the
end (I'm not on Windows, where, according to the man page, seek() is
broken).
## Generate data with a repeated easy-to-recognize byte pattern
## of length 26:
mydata <- rep(charToRaw(paste(letters, collapse="")), 400)
## Write the data to test.gz file:
con <- gzfile("test.gz", open="wb")
writeBin(mydata, con)
close(con)
## Read the data from test.gz file. We'll read blocks of 26 bytes
## located at various offsets that are multiple of 26, so we expect
## to see our original pattern ("abc...xyz").
con <- gzfile("test.gz", open="rb")
## Offset 0: ok
> rawToChar(readBin(con, "raw", n=26))
[1] "abcdefghijklmnopqrstuvwxyz"
## Offset 78: still ok
> seek(con, where=78)
[1] 26
> seek(con)
[1] 78
> rawToChar(readBin(con, "raw", n=26))
[1] "abcdefghijklmnopqrstuvwxyz"
## Offset 520: data is messed up
> seek(con, where=520)
[1] 104
> seek(con)
[1] 520
> rawToChar(readBin(con, "raw", n=26))
[1] "zabcdefghijklmnopqrstuvvuv"
## Offset 2600: very messed up
> seek(con, where=2600)
[1] 546
> seek(con)
[1] 2600
> rawToChar(readBin(con, "raw", n=26))
[1] "xxxxxmpxxxxxxesxxxxxxxxxxp"
## Offset 10400: see previous email (subject: "error when calling
## seek() twice on a gzfile connection")
> seek(con, where=10400)
[1] 2626
Warning message:
In seek.connection(con, where = 10400) :
seek on a gzfile connection returned an internal error
close(con)
Reading the data sequentially with no calls to seek() returns the
expected pattern 400 times:
con <- gzfile("test.gz", open="rb")
blocks <- sapply(1:400, function(i) rawToChar(readBin(con, "raw", n=26)))
## Check the result:
> readBin(con, "raw", n=26) # no more data
raw(0)
> seek(con)
[1] 10400
> table(blocks)
blocks
abcdefghijklmnopqrstuvwxyz
400
Thanks,
H.
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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