GO.db installation error
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cananhas • 0
@cananhas-11660
Last seen 4.9 years ago

Hi everyone,

I try to install GO.db. However, I get following error although there is no internet connection problem. What could be an alternative solution?

Thanks in advance,

Canan

 biocLite("GO.db")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.1.2.
Installing package(s) 'GO.db'
trying URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.1/GO.db_3.0.0.zip'
Content type 'application/zip' length 56875847 bytes (54.2 Mb)
opened URL
downloaded 15.6 Mb

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 16330868 != reported length 56875847
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
 

 

GO go.db • 727 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

R-3.1.2 is from October 2014, which means that the GO data you are planning to download is from fall 2014 as well. That's pretty old data, especially in the context of gene annotations, so there really isn't much profit in trying to get data from two years ago. Unless of course you are trying to recapitulate some old analyses that you don't want to change.

Anyway, we don't support old versions of Bioconductor, so you should install the current versions of R and Bioc. If you have problems with that, please let us know.
 

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@martin-morgan-1513
Last seen 9 weeks ago
United States

The package size is 54.2 Mb, but only 15.6 is downloaded, so somehow the download has been truncated. The file is actually 54.2Mb; you could troubleshoot the download problem (best in the long run) or try downloading it from the url in the post above (e.g., via your browser) outside of R, and then install.packages("GO.db_3.0.0.zip", repos=NULL, type="binary"). (I'm not 100% sure of the install.packages command).

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cananhas • 0
@cananhas-11660
Last seen 4.9 years ago

I will try both ways. Thank you so much for your replies.

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