Error in loading R package "GO.db" in installing WGCNA R package

Question

[zaynabmousavian]

Hi all,

When I have tried to install package dependencies of WGCNA, I have got the following error in the step of loading GO.db package after download completed:

 

biocLite(c("GO.db")) 
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'GO.db'
trying URL 'http://bioconductor.org/packages/2.13/data/annotation/src/contrib/GO.db_2.10.1.tar.gz'
Content type 'application/x-gzip' length 26094175 bytes (24.9 Mb)
opened URL
==================================================
downloaded 24.9 Mb

* installing *source* package âGO.dbâ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: match.arg(synchronous, c("off", "normal", "full"))
  error: 'arg' must be NULL or a character vector
Error: loading failed
Execution halted
ERROR: loading failed
* removing â/home/zmousavian/R/x86_64-pc-linux-gnu-library/3.0/GO.dbâ

The downloaded source packages are in
        â/tmp/RtmpBDs1Tq/downloaded_packagesâ
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package âGO.dbâ had non-zero exit status
2: installed directory not writable, cannot update packages 'colorspace',
  'lattice', 'mgcv', 'survival' 

 

Can anyone help me to solve this problem?

Thanks

Answer 1

[Martin Morgan]

The current version of RSQLite is not backward compatible with your older version of R / Bioconductor. Your options are to either use a current version of R (and hence Bioconductor) or to use an old version of RSQLite, as explained here. It is better in the long term to use a current version of R.

Answer 2

[andrew]

Agreed.  The latest GO.db package in Bioconductor 3.0 requires R 3.1.2

By the way, we will feature the latest GO methodology in iPathwayGuide with our visualizations in an upcoming release (April).

[zaynabmousavian]

Thanks, but how can I install this version of R in linux?