Hi,

Could anyone help me with the following problem?

I work on university's HPC (High Performance Computing) as a normal user without admin rights. I tried to install package Rsubread. The installation was successful. But there were some message which said "installation path not writeable, unable to update packages".

Not sure this is serious or not? How to fix it if needed?

Thanks!

> BiocManager::install("Rsubread", version = "3.8")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)
Installing package(s) 'Rsubread'
trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/Rsubread_1.32.4.tar.gz'
Content type 'application/x-gzip' length 9410919 bytes (9.0 MB)

downloaded 9.0 MB

* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Linux.
** libs
......
......
installing to /scratch/RDS-FSC-WLR6411-RW/longsonghome/R/packages/Rsubread/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsubread)

The downloaded source packages are in
        ‘/tmp/pbs.3100355.pbsserver/RtmpHIn1GU/downloaded_packages’
installation path not writeable, unable to update packages: distrEx, insight,
  MASS, rJava, rlang, survival
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)

Matrix products: default
BLAS: /usr/local/R/3.5.2/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R/3.5.2/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] 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_1.30.4 compiler_3.5.2     tools_3.5.2

You don't have permission to write to the computer's system areas, which is where R itself is installed, so you need to install the package to a directory in your own disk area. For example, you might create a directory RLibs to hold this and any other R packages you might want to install:

system("mkdir RLibs")
install("Rsubread", lib="RLibs")
library(Rsubread, lib.loc="RLibs")