Search
Question: Error using biocLite
0
gravatar for christina.fjeldbo
19 months ago by
christina.fjeldbo10 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 19 months ago by Martin Morgan ♦♦ 22k • written 19 months ago by christina.fjeldbo10

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 19 months ago by Walter F. Baumann 10
0
gravatar for Martin Morgan
19 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 19 months ago by Martin Morgan ♦♦ 22k

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

ADD REPLYlink written 19 months ago by christina.fjeldbo10

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        

 

ADD REPLYlink written 10 days ago by khp30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 155 users visited in the last hour