error while installing " BSgenome.Hsapiens.UCSC.hg19"
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@pegahtaklifi-24293
Last seen 9 weeks ago
Iran

Hello I am trying to install BSgenome.Hsapiens.UCSC.hg19 on Rstudio with R version 4.0.3 using the command below

BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")

I get an error and several warning messages

Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 48644749 != reported length 710245413
2: In download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://bioconductor.org/packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.3.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘BSgenome.Hsapiens.UCSC.hg19’ failed
Old packages: 'nlme'

I wonder how I could solve this I would really appreciate your help

BSgenome.Hsapiens.UCSC.hg19 • 1.2k views
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5
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@martin-morgan-1513
Last seen 10 weeks ago
United States

The key part of the error is actual in the warning

Timeout of 60 seconds was reached

and the solution is to increase the timeout documented on ?download.file with

options(timeout = 300)  # is 5 minutes enough?

and then trying again

BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
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0
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Thank you! so I found out my internet is really slow today so I downloaded the package separately and installed it manually in R. all fine

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Thanks, @martin-morgan-1513. This helped download it.

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Yes, this worked

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