Warning in downloading GSE data from ncbi

Question

[hasani.iut6]

I'm trying to downloading GSE49710 series data from ncbi to R by using the getGEO() function that is belong to the GEOquery package in R software.

I've been used following code for downloading the data:

micro=getGEO("GSE49710",destdir = "GSE49710/")

and I've faced with the following warnings():

Warning messages:
1: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
2: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
3: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
4: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
5: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
6: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
7: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
8: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
9: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
10: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
11: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
12: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
13: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
14: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
15: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
16: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
17: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
18: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
19: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
20: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
21: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
22: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
23: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
24: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
25: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
26: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
27: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
28: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
29: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
30: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
31: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
32: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
33: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
34: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
35: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
36: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
37: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
38: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
39: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
40: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
41: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
42: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
43: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
44: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
45: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
46: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
47: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
48: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
49: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error
50: In readLines(con, n = chunksize) :
  seek on a gzfile connection returned an internal error

I think that these warning caused that the data won't be downloaded completely.

I've googled for this warning a lot and I've founded a lot of people that have the same problem but I can't find solution for this warning.

How can I solve it?

The output of sessionInfo of R is:

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

Answer 1

[Giovanni M Dall'Olio]

I've downloaded this dataset in my computer and I didn't get any warning.

In any case it doesn't seem a problem with the download, but rather some warning due to the gzip library used in GEOquery. In any case if you have doubts you can download the file manually and see if you get the same warning when you parse it from disk:

$: wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49710/matrix/GSE49710_series_matrix.txt.gz
$: R
> micro.downloaded = parseGEO("myfolder/GSE49710_series_matrix.txt.gz")
> micro.GEOquery = getGEO("GSE49710")

Which version of the zlib library are you using? I think you can get it from ```man zlib```. I am using Version 1.2.8 here.

[hasani.iut6]

My zlib version is as same as you. I downloaded the data to my laptop and then loaded them to R and I steel get the warning

[hasani.iut6]

I just updated R and all packages and the problem was solved .