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Question: How to install or update old packages of Bioconductor in R
0
gravatar for Sat
6 weeks ago by
Sat0
Sat0 wrote:

hi,

I am new this package.

I tried to install bioconductor in R (Version 1.0.153) for differential gene expression analysis.

> ## try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Old packages: 'boot', 'Matrix', 'mgcv'
Update all/some/none? [a/s/n]: 

and tried these commands too...

Installing package into ‘/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1’
Update all/some/none? [a/s/n]: 
(as ‘lib’ is unspecified)
Update all/some/none? [a/s/n]: 
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocInstaller_1.15.5.tar.gz'
Update all/some/none? [a/s/n]: 
Content type 'application/x-gzip' length 14144 bytes (13 Kb)
Update all/some/none? [a/s/n]: 
opened URL
Update all/some/none? [a/s/n]: 

this is what i got. what to do next, how to install or update these old packages.

Help me to update the required packages.

thank you

ADD COMMENTlink modified 6 weeks ago by shepherl ♦♦ 510 • written 6 weeks ago by Sat0
0
gravatar for shepherl
6 weeks ago by
shepherl ♦♦ 510
shepherl ♦♦ 510 wrote:
Update all/some/none? [a/s/n]:

Is asking for user input of a (to update all) or s (to update some packages) or n (to update none of the packages), To update all outdated packages type a when this is prompted.

> source("https://bioconductor.org/biocLite.R")
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Old packages: 'boot', 'Matrix', 'mgcv'
Update all/some/none? [a/s/n]:

So you would type a followed by carriage return

Update all/some/none? [a/s/n]: a

If there is some ERROR that occurs after you do this plesae include it in your question.

ADD COMMENTlink written 6 weeks ago by shepherl ♦♦ 510
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