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seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
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getGEO("GSExxxx") error #34

Closed YairGatt closed 8 years ago

YairGatt commented 8 years ago

Hello, Retrieving data from GEO in the form of getGEO("GSExxxx") seems to produce errors that didn't occur before. Perhaps this is due to NCBI's recent move from http to https?

>GSE <- getGEO("GSE3105")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE3nnn/GSE3105/matrix/

Found 1 file(s)
GSE3105_series_matrix.txt.gz

% Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  251k  100  251k    0     0  70762      0  0:00:03  0:00:03 --:--:-- 70753
File stored at:
/tmp/RtmpnbTgfV/GPL199.soft
Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
  invalid 'nlines' argument

Is this a known issue? Yair

seandavi commented 8 years ago

Hi, @YairGatt. Please make sure you are using the latest GEOquery. If you have problems after upgrading, could you also send the output of sessionInfo()? You are probably correct that this is related to the change to https, but that has been addressed in GEOquery's later versions.

YairGatt commented 8 years ago

Thank you for your swift reply. After updating to the latest versions of R (3.3.1), Bioconductor (3.4) and GEOquery (2.40.0), everything is working fine!

seandavi commented 8 years ago

Great. Thanks for closing the loop.