[BioC] rsqlite for windows from fhcrc

Martin Morgan mtmorgan at fhcrc.org
Fri Aug 22 22:50:01 CEST 2014

Hi Kasper --

On 08/21/2014 07:08 PM, Kasper Daniel Hansen wrote:
> I have had an off-list email exchange with a user about installing minfi
> and therefore RSQLite for Windows.  Now, there has been quite a few emails
> back and forth and I am not sure the user is doing everything by the book,
> but based on the log message it appears that you can run
>    BiocInstaller 1.14.2
>    R 3.1.0 (Windows)
> and then do
>    biocLite("RSQLite")
> which fetches version 0.11.4 from cran.fhcrc.org and still get
>    R> library(RSQLite)
> Error: package 'RSQlite' was built before R 3.0.0: please reinstall it.
> (details being transcribed from a PNG screenshot so there may be typing
> mistakes; I am happy to send screen shot).
> My initial reaction is that this sound wrong (on the user side), but I now
> have a session transcription and it looks a bit fishy.  Can anyone check
> this?

The binary was built under 3.1.1, and installing under 3.1.0 generates a 
_warning_ about the mis-match between 3.1.0 and 3.1.1.

It seems like biocLite() (if it's successful?) is writing to one library, and 
library() is reading from another. Perhaps .libPaths() in addition to 
information about permissions on each directory would help, e.g., if the user 
writeable library comes second, and there is already a version in the system 
library??. One can provide a 'lib' argument to both biocLite and to library to 
ensure that the both reference the same location.


> Best,
> Kasper
> 	[[alternative HTML version deleted]]
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