Cannot load or update GO.db
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Entering edit mode
@steve-pederson-3490
Last seen 8 months ago
Australia

Hi,

I cannot load or update the package GO.db & can't quite figure a way out of it. I've tried as superuser & a regular user & the installation fails on both attempts.

Below is the output after running "R --vanilla" as superuser

Thanks,

Steve

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.4), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("GO.db")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.4), R version 3.2.0.
Installing package(s) 'GO.db'
trying URL 'http://bioconductor.org/packages/3.0/data/annotation/src/contrib/GO.db_3.0.0.tar.gz'
Content type 'application/x-gzip' length 28747892 bytes (27.4 MB)
==================================================
downloaded 27.4 MB

* installing *source* package ‘GO.db’ ...
** 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: ls(envir, all.names = TRUE)
  error: 2 arguments passed to .Internal(ls) which requires 3
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/GO.db’
* restoring previous ‘/usr/local/lib/R/site-library/GO.db’

The downloaded source packages are in
    ‘/tmp/Rtmpsb2vZH/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘GO.db’ had non-zero exit status
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.16.4

loaded via a namespace (and not attached):
[1] tools_3.2.0

 

GO.db bioclite • 3.3k views
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3
Entering edit mode
@steve-pederson-3490
Last seen 8 months ago
Australia

After a bit of playing around it's now installed & loading. Running biocValid(fix=TRUE) sorted it out.

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1
Entering edit mode

ahhhh thanks! that fixed it for me as well

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