Question: Warning in downloading GSE data from ncbi
0
gravatar for hasani.iut6
5.2 years ago by
hasani.iut660
Iran, Islamic Republic Of
hasani.iut660 wrote:

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

geoquery warning ncbi • 1.9k views
ADD COMMENTlink modified 5.2 years ago by Giovanni M Dall'Olio27k • written 5.2 years ago by hasani.iut660
0
gravatar for Giovanni M Dall'Olio
5.2 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

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.

ADD COMMENTlink written 5.2 years ago by Giovanni M Dall'Olio27k

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

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.2 years ago by hasani.iut660

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

ADD REPLYlink written 5.2 years ago by hasani.iut660
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