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Question: GO.db installation error
0
gravatar for cananhas
14 months ago by
cananhas0
cananhas0 wrote:

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")) :
 

 

ADD COMMENTlink modified 14 months ago • written 14 months ago by cananhas0
0
gravatar for James W. MacDonald
14 months ago by
United States
James W. MacDonald45k wrote:

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.
 

ADD COMMENTlink written 14 months ago by James W. MacDonald45k
0
gravatar for Martin Morgan
14 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

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).

ADD COMMENTlink written 14 months ago by Martin Morgan ♦♦ 21k
0
gravatar for cananhas
14 months ago by
cananhas0
cananhas0 wrote:

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

ADD COMMENTlink written 14 months ago by cananhas0
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