Question: Cannot load or update GO.db
gravatar for Steve Pederson
3.7 years ago by
Steve Pederson140 wrote:


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



> source("")
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
> biocLite("GO.db")
Using Bioconductor version 3.0 (BiocInstaller 1.16.4), R version 3.2.0.
Installing package(s) 'GO.db'
trying URL ''
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
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)

 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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 • 2.7k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Steve Pederson140
Answer: Cannot load or update GO.db
gravatar for Steve Pederson
3.7 years ago by
Steve Pederson140 wrote:

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

ADD COMMENTlink written 3.7 years ago by Steve Pederson140

ahhhh thanks! that fixed it for me as well

ADD REPLYlink written 3.7 years ago by asmussennc10
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