Working w/ netReg to make Regression Models for Methylation

[Spencer_Brackett]

Hello,

I am attempting to generate regression models that display the expression of methylation for a TCGA dataset. Unfortunately, I am running into some problems with starting this in R Studio. I am running this object on my Windows 10 and seem to be experiencing permission problems (see final lines). How should I proceed?

> BiocManager::install("netReg")

Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)

Installing package(s) 'BiocVersion', 'netReg'

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/BiocVersion_3.8.0.zip'

Content type 'application/zip' length 8843 bytes

downloaded 8843 bytes

trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/netReg_1.6.0.zip'

Content type 'application/zip' length 4143315 bytes (4.0 MB)

downloaded 4.0 MB

package ‘BiocVersion’ successfully unpacked and MD5 sums checked

package ‘netReg’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\Spencer\AppData\Local\Temp\RtmpW6FwPY\downloaded_packages

installation path not writeable, unable to update packages: class, cluster, codetools, foreign,

  lattice, MASS, Matrix, mgcv, nlme, rpart, survival

Best,

Spencer

[EconomiCurtis]

As you note, the important error message is installation path not writeable, unable to update packages

This suggests a permissions issue. There's some advice here.

installation path not writable R, unable to update packages

Also, I think this issue pops up most frequently with bioconductor package installation. You might search their community forum for advice https://support.bioconductor.org/