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Question: Error using biocLite
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gravatar for christina.fjeldbo
16 months ago by
christina.fjeldbo0 wrote:

Hi,

 

I have problems using the biocLite.

When using: biocLite(org.Hs.eg.db)

this error appears:

'no packages in repository (no internet connection?)' while trying https://bioconductor.org/packages/3.2/bioc, trying https://bioconductor.org/packages/3.1/bioc
Error: no packages in repository (no internet connection?)

 

Output from sessionInfo()

sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows XP (build 2600) Service Pack 3

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.0

 

 

 

ADD COMMENTlink modified 16 months ago by Martin Morgan ♦♦ 22k • written 16 months ago by christina.fjeldbo0

It should be biocLite("org.Hs.eg.db") (with quotation marks)... However, I just tried it and it works as expected, but I use R 3.3.1. 

ADD REPLYlink written 16 months ago by Walter F. Baumann 10
0
gravatar for Martin Morgan
16 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Provide the full transcript -- Does

source("https://bioconductor.org/biocLite.R")

work? What about using http:// instead of https://?

options(BioC_mirror="http://bioconductor.org")
biocLite("org.Hs.eg.db")
ADD COMMENTlink written 16 months ago by Martin Morgan ♦♦ 22k

Thanks! Including the options(BioC_mirror="http://bioconductor.org") resolved it.

ADD REPLYlink written 16 months ago by christina.fjeldbo0
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