Question

when using getGEO() from GEOquery, an error happened : a file does not exist

1

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jing ▴ 20

@jing-24653

Last seen 3.2 years 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 • 1.3k views

ADD COMMENT • link updated 3.2 years ago by Sean Davis 21k • written 3.2 years ago by jing ▴ 20

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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.

ADD REPLY • link 3.2 years ago Sean Davis 21k

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

ADD REPLY • link 3.2 years ago jing ▴ 20

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

ADD REPLY • link 3.2 years ago Sean Davis 21k

score 1 · Answer 1 · 2021-01-27

1

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Sean Davis 21k

@sean-davis-490

Last seen 3 months 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.

ADD COMMENT • link 3.2 years ago Sean Davis 21k