Question: Edge R 3.16.5 Installation pathway issues/unable to update required packages
0
gravatar for ozburn
22 months ago by
ozburn0
ozburn0 wrote:

I am trying to download the EdgeR 3.16.5 package on R. 3.3.3 and I consistently get the following error text

source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install
> biocLite(edgeR)
Error in match(x, table, nomatch = 0L) : object 'edgeR' not found
> biocLite("edgeR")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Installing package(s) ‘edgeR’
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.3/edgeR_3.16.5.tgz'
Content type 'application/x-gzip' length 1747625 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

The downloaded binary packages are in
    /var/folders/vh/c4vpsdbj5dv73r6z3ylyg3xdf1hlfv/T//RtmphOVoWw/downloaded_packages
installation path not writeable, unable to update packages: boot, cluster, foreign, lattice, MASS, Matrix, mgcv, rpart, survival 

I have checked for updates for the packages and run updates. And those run fine. I have also tried updating the listed packages individually with a similar error output. 

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.3
edger run_edger • 358 views
ADD COMMENTlink modified 22 months ago by James W. MacDonald51k • written 22 months ago by ozburn0
Answer: Edge R 3.16.5 Installation pathway issues/unable to update required packages
2
gravatar for James W. MacDonald
22 months ago by
United States
James W. MacDonald51k wrote:

The only error text is when you tried to use biocLite with a non-character package name. Otherwise there isn't an error. You do get a notice that says this:

installation path not writeable, unable to update packages: boot, cluster, foreign, lattice, MASS, Matrix, mgcv, rpart, survival 

Which has nothing to do with edgeR. Instead, it is saying that these packages, which come with R, have been installed in a directory for which you do not have write privileges. This is because you apparently installed R using sudo, and now are running as a regular user. If you want to update those packages, you need to run R under sudo.

In addition, you are using an old version of R and Bioconductor. You should update to R-3.4.2 and the current release version of Bioconductor.

ADD COMMENTlink written 22 months ago by James W. MacDonald51k
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