Installation Path Not Writeable
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@srinivasansandiego-23147
Last seen 4.1 years ago

I am getting this error when I install Bioconductor in R Studio in Linux 18.10

> if (!requireNamespace("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
> BiocManager::install()
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installation path not writeable, unable to update packages: foreign, nlme

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.3      tools_3.6.3

I would appreciate any help to resolve this. Thanks.

R BioConductor • 1.8k views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

First off, that's not an error. It's a warning. An error is when R cannot do something you asked it to do. But you didn't try to update either foreign or nlme, did you?

You get this warning because you are using a centrally-installed R that has a library directory that isn't writeable by a non-privileged user. This isn't an unusual situation, and unless one of the recommended packages has some pernicious bug (which isn't likely - they have been around since like 1995 or whatever, and have been tested by literally millions of users), you won't ever need to do anything to them anyway.

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