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Question: TCGABiolinks not available for R3.3.0
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2.4 years ago by
j.ritchie0 wrote:

Hi

Can you help me? Im trying to install TCGA Biolinks. I tried to install it through the Install Packages option of R Studio through the CRAN mirror through the Install Packages option in the Tools menu:

Warning in install.packages :
package ‘TCGAbiolinks’ is not available (for R version 3.3.0)

I have tried this code from previous posts of people who have had this problems in previous versions of R:

> remove.packages("BiocInstaller")

Removing package from ‘C:/Users/Judith Valluru/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
> source("http://bioconductor.org/biocLite.R")
Installing package into ‘C:/Users/Judith Valluru/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/BiocInstaller_1.22.2.zip'
Content type 'application/zip' length 119385 bytes (116 KB)

package ‘BiocInstaller’ successfully unpacked and MD5 sums checked

C:\Users\Judith Valluru\AppData\Local\Temp\RtmpsRpR3K\downloaded_packages

I then tried to install it again by the same route but got the original error message.

Im using R 3.3.0 and only recently installed R studio.

I am not an expert by far in R but dont know what to try next. Could anyone help?

Thanks

modified 2.4 years ago by Martin Morgan ♦♦ 22k • written 2.4 years ago by j.ritchie0

You show things you have done, but not the important part! I got TCGAbiolinks to install without problem on a Windows box running R-3.3.0, so it's doable. You need to show the output from

biocLite("TCGAbiolinks")

all the way up to the warning message.

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.2), ?biocLite for help
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.2), R 3.3.0 (2016-05-03).
Content type 'application/zip' length 32094194 bytes (30.6 MB)

package TCGAbiolinks successfully unpacked and MD5 sums checked

Old packages: 'GenomicAlignments', 'GenomicRanges', 'limma', 'rtracklayer'
Update all/some/none? [a/s/n]: n
> 

I entered

biocLite("TCGAbiolinks")

It installed a lot of packages as you  advised, , each component installed successfully, and it ended advising me where the binary packages were stored and asking me about updating old packages. However when I was in the process of copyign this into this reply my darn computer decided to restart itself automatically to install updates and I didnt have the chance to stop it so I lost the entire output. When I opened r studio again it was all gone. Argh so exasperating! Thank you for your help.