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Question: TCGABiolinks not available for R3.3.0
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gravatar for j.ritchie
17 months ago by
j.ritchie0
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)
downloaded 116 KB

package ‘BiocInstaller’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    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 

ADD COMMENTlink modified 17 months ago by Martin Morgan ♦♦ 20k • written 17 months 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.

ADD REPLYlink written 17 months ago by James W. MacDonald45k

I was able to install TCGAbiolinks successfully. Can you please add to your original post the output like the following, from your session, and then post a COMMENT indicating that you have updated your question? I notice that you have 'Biolinks' in the title of your post, whereas the package has a lowercase 'b' in its name. (Actually, on first attempt this installed a very large number of packages; feel free to edit to include the most important information -- the lines including biocLite() and immediately after, sohw the version of Bioconductor and BiocInstaller being used and if it gets that far some of the url's that packages, especially Bioconductor packages with bioconductor.org in the path, are being downloaded from).

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.2), ?biocLite for help
> biocLite("TCGAbiolinks")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.2), R 3.3.0 (2016-05-03).
Installing package(s) ‘TCGAbiolinks’
trying URL 'https://bioconductor.org/packages/3.3/bioc/bin/windows/contrib/3.3/TCGAbiolinks_1.2.5.zip'
Content type 'application/zip' length 32094194 bytes (30.6 MB)
downloaded 30.6 MB

package ‘TCGAbiolinks’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\mtmorgan\AppData\Local\Temp\16\Rtmp2xiFj1\downloaded_packages
Old packages: 'GenomicAlignments', 'GenomicRanges', 'limma', 'rtracklayer'
Update all/some/none? [a/s/n]: n
> 
ADD REPLYlink written 17 months ago by Martin Morgan ♦♦ 20k

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. 

ADD REPLYlink written 17 months ago by j.ritchie0

Next time around it won't have to install all those packages, so it should be much quicker.

ADD REPLYlink written 17 months ago by Martin Morgan ♦♦ 20k
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