when using getGEO() from GEOquery, an error happened : a file does not exist
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jing ▴ 20
@jing-24653
Last seen 6 months ago
library(GEOquery)
gse = "GSE42872"
eSet <- getGEO(gse, 
               destdir = '.', 
               getGPL = F)

Found 1 file(s) GSE42872_series_matrix.txt.gz Using locally cached version: ./GSE42872_series_matrix.txt.gz

error: 'C:\Users\kktt\AppData\Local\Temp\Rtmpovt65s\file1db02805191' does not exist.

any help?

Thanks!

GEOquery projectR • 302 views
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If you restart R and try again, does that help? The error seems to imply that the Temp directory does not exist.

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thanks a lot! I have found my problem and solved it

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Great to hear that you got things worked out, @jing-24653. I posted your solution as an answer.

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@sean-davis-490
Last seen 18 days ago
United States

Thanks for help from a dedicated user who tracked down this issue to using a Chinese username on Windows and misnamed Temp directory. The solution seems to involve changing the Microsoft Windows username to English.

See the associated Github Issue for discussion and details.

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