Question

Error using biocLite

0

Entering edit mode

christina.fjeldbo ▴ 10

@christinafjeldbo-12642

Last seen 7.6 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 • 2.4k views

ADD COMMENT • link updated 7.7 years ago by Martin Morgan 25k • written 7.7 years ago by christina.fjeldbo ▴ 10

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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.

ADD REPLY • link 7.7 years ago Walter F. Baumann ▴ 10

score 0 · Answer 1 · 2017-03-20

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months 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")

ADD COMMENT • link 7.7 years ago Martin Morgan 25k

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

ADD REPLY • link 7.7 years ago christina.fjeldbo ▴ 10

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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

ADD REPLY • link 6.1 years ago khp ▴ 30