Question: installation of Biocunductor packages in My home directory.
0
gravatar for vinod.acear
12 months ago by
vinod.acear30
India
vinod.acear30 wrote:

I have two R installed

1. on a cluster admin account that has "R" (/home/vs580/R/x86_64-pc-linux-gnu-library/3.4 ) directory in my home to contain some locally installed packages.

2. Because of permission issues, I have installed R locally in "home/vs580/My_R/"

But when I install Bioconductor packages in my local home "home/vs580/My_R/R/3.4.4/lib64/R/library"

## try http:// if https:// URLs are not supported

source("http://bioconductor.org/biocLite.R")

biocLite("BSgenome", lib="/home/vs580/My_R/R/3.4.4/lib64/R/library")

I am getting following error

> biocLite("BSgenome", lib="/home/vs580/My_R/R/3.4.4/lib64/R/library")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.4 (2018-03-15).

Installing package(s) ‘BSgenome’

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/BSgenome_1.44.2.tar.gz'

Content type 'application/x-gzip' length 6064725 bytes (5.8 MB)

==================================================

downloaded 5.8 MB

 

* installing *source* package ‘BSgenome’ ...

** R

** inst

** preparing package for lazy loading

Error: package or namespace load failed for ‘GenomeInfoDb’ in dyn.load(file, DLLpath = DLLpath, ...):

unable to load shared object '/home/vs580/R/x86_64-pc-linux-gnu-library/3.4/RCurl/libs/RCurl.so':

  libimf.so: cannot open shared object file: No such file or directory

Error : package ‘GenomeInfoDb’ could not be loaded

ERROR: lazy loading failed for package ‘BSgenome’

* removing ‘/home/vs580/My_R/R/3.4.4/lib64/R/library/BSgenome’

 

The downloaded source packages are in

    ‘/tmp/Rtmpda3u6V/downloaded_packages’

Updating HTML index of packages in '.Library'

Making 'packages.html' ... done

Warning message:

In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘BSgenome’ had non-zero exit status

  

ADD COMMENTlink written 12 months ago by vinod.acear30

This looks like a problem with RCurl; does library(RCurl) work for you?

ADD REPLYlink written 12 months ago by Martin Morgan ♦♦ 23k
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