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Question: Problems Installing biomaRt
0
gravatar for christopher.mcfall
3 months ago by
christopher.mcfall0 wrote:

I've tried to install biomaRt using the code below (arch linux OS) but it doesn't appear to be working:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")

If anyone can lend a had, I'd appreciate it.

#Console:

###############################################################3

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
> biocLite("biomaRt")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) ‘biomaRt’
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/biomaRt_2.34.2.tar.gz'
Content type 'application/x-gzip' length 281204 bytes (274 KB)
==================================================
downloaded 274 KB

* installing *source* package ‘biomaRt’ ...
** R
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/arch/R/x86_64-pc-linux-gnu-library/3.4/stringi/libs/stringi.so':
  libicui18n.so.60: cannot open shared object file: No such file or directory
ERROR: lazy loading failed for package ‘biomaRt’
* removing ‘/home/arch/R/x86_64-pc-linux-gnu-library/3.4/biomaRt’

The downloaded source packages are in
    ‘/tmp/Rtmp0FccLg/downloaded_packages’
installation path not writeable, unable to update packages: cluster, Matrix, nlme, survival
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘biomaRt’ had non-zero exit status

ADD COMMENTlink modified 3 months ago • written 3 months ago by christopher.mcfall0
0
gravatar for Mike Smith
3 months ago by
Mike Smith2.8k
EMBL Heidelberg / de.NBI
Mike Smith2.8k wrote:

It looks like this problem really lies with the stringi package.  It'd suggest reinstalling that as a first try, and then re-running the biomaRt installation:

install.packages('stringi')

It looks like that has a system dependency on ICU4C, so if you still encounter error it may be that you need to install that via the Arch package manager. My Arch is pretty rusty, but I guess it's this you need.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Mike Smith2.8k
0
gravatar for christopher.mcfall
3 months ago by
christopher.mcfall0 wrote:

Hi Mike. Nicely done. Thank you for your help on this. That seems to have fixed everything. 

Best,

Christopher

ADD COMMENTlink written 3 months ago by christopher.mcfall0
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