Hi,

I am trying to install GO.db and am getting the error "installation of package ‘GO.db’ had non-zero exit status". Full output and session info below:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> 
> biocLite("GO.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘GO.db’
installing the source package ‘GO.db’

trying URL 'https://bioconductor.org/packages/3.3/data/annotation/src/contrib/GO.db_3.3.0.tar.gz'
Content type 'application/x-gzip' length 32027913 bytes (30.5 MB)
downloaded 30.5 MB

'\\fs-home-j\home-001\bsp022\My' is not recognized as an internal or external command,
operable program or batch file.

The downloaded source packages are in
	‘C:\Users\bsp022\AppData\Local\Temp\RtmpMdl5gA\downloaded_packages’
Warning messages:
1: running command '"//fs-home-j/home-001/bsp022/My Documents/R/R-3.3.1/bin/x64/R" CMD INSTALL -l "\\fs-home-j\home-001\bsp022\My Documents\R\R-3.3.1\library" C:\Users\bsp022\AppData\Local\Temp\RtmpMdl5gA/downloaded_packages/GO.db_3.3.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GO.db’ had non-zero exit status

> traceback()
No traceback available 

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] tools_3.3.1

I have seen several answers to similar problem that mention an incompatiblity with RSQLite, but I don't think that this is the case here: I have updated everything and am using RSQLite 1.0.0, R3.3.1 and bioconductor 3.3. I have also run biocValid to check packages are of the right versions:

> biocValid()   
[1] TRUE

The error has to do with the space in your .libPaths (the 'My Documents' part). But I have a space in mine as well:

> .libPaths()
[1] "c:/Program Files/R/R-3.3.0/library"

So it can't just be that. The //fs-home-j/home-001/bsp022/ business makes me think you have cygwin installed (which I do not), so that might be the problem. I instead have RTools installed, which doesn't appear to have problems with spaces in the path.

It used to be that you needed cygwin to compile R and source packages on Windows, but these days it's been superceded by the RTools package. If you don't need cygwin, you might try uninstalling it and then installing RTools to see if that helps. Otherwise, you might want to check on R-help to see if they have any advice, as this seems to have more to do with R not wanting to install into a path with spaces, rather than a Bioconductor-centric problem.