Error using biocLite
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@christinafjeldbo-12642
Last seen 5.4 years ago

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

 

 

 

bioconductor • 1.8k views
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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. 

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@martin-morgan-1513
Last seen 21 days ago
United States

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

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Hello, 

I'm trying to install phyloseq and am having the same error: 

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

#Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help

 biocLite('phyloseq')
Error: 'no packages in repository (no internet connection?)' while trying https://bioconductor.org/packages/3.7/bioc

I tried the way you suggested here, but get the same error.

 

 options(BioC_mirror="http://bioconductor.org")
> biocLite("org.Hs.eg.db")
Error: 'no packages in repository (no internet connection?)' while trying http://bioconductor.org/packages/3.7/bioc

I do have internet connection. I would appreciate your help with this. 

 

Other information:

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

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

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

other attached packages:
[1] BiocInstaller_1.30.0 dada2_1.9.2          Rcpp_0.12.19        

 

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