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Old 06-04-2011, 09:43 PM   #1
akolman
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Location: Cambridge, MA

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Default GEOquery error message

Hello,

I am using Windows 7 and R 2.12.2

When I try to run these two lines I get the following error from getGEO

library(GEOquery)
GSE7562 <- getGEO("GSE7562")

Found 1 file(s) GSE7562_series_matrix.txt.gz Error in file(con, "r") : cannot open the connection In addition: Warning messages: 1: In download.file(sprintf("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/%s/%s", : download had nonzero exit status 2: In file(con, "r") : cannot open file 'C:\Users\APD\AppData\Local\Temp\RtmptmeDAb/GSE7562_series_matrix.txt.gz': No such file or directory

Am I missing something to get GEOquery working?

Thanks in advance,
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Old 06-05-2011, 01:19 PM   #2
maubp
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Can you get to this file manually, e.g. in your browser:
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/..._matrix.txt.gz

That is what I believe geoquery is trying to download. Its about 2.5MB so quite small. I'm finding the FTP site works but is a bit slow....
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Old 06-05-2011, 02:55 PM   #3
akolman
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Thanks. I downloaded the file but I still have the same error. Then, I went to the GEO Accession viewer and downloaded the file in .soft format. That seems to work. I would be a little disappointed if I have to these all the time.
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Old 06-05-2011, 02:58 PM   #4
maubp
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What version of geoquery do you have? I notice your R is a little out of date.
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Old 06-05-2011, 02:59 PM   #5
akolman
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I have version 2.17.5
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Old 06-05-2011, 03:21 PM   #6
maubp
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The current version is geoquery 2.18.0, that might fix this...
http://bioconductor.org/packages/rel.../GEOquery.html
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Old 06-05-2011, 03:30 PM   #7
akolman
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This is somewhat unrelated. How can I update R and without losing all the packages I have installed?

I tried installing the newer version of GEOquery but it does work with my current R version.
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Old 06-05-2011, 10:56 PM   #8
maubp
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Quote:
Originally Posted by akolman View Post
This is somewhat unrelated. How can I update R and without losing all the packages I have installed?
I don't think you can - the R API is likely to change between major releases. There might be a neat way to get a list of all the installed libraries, to make re-installing the same set easier - they can be installed via the R command line as well as via the R GUI.
Quote:
Originally Posted by akolman View Post
I tried installing the newer version of GEOquery but it does work with my current R version.
Try asking Sean Davis directly about this error. Also, if it was a network problem, it might go away on its own - have you re-tried at a different time of day?
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Old 06-06-2011, 07:26 AM   #9
akolman
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I updated R and installed the newest version of GEOquery, and I still get the same error message. Anyway, I think I can get away not using the getGEO function to download the files.
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