[Bioc-sig-seq] GenomicFeatures package

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Nov 2 18:09:26 CET 2009

On Nov 2, 2009, at 11:52 AM, Seth Falcon wrote:
> Enabled RTREE is now the default for RSQLite and there is no plan to  
> change that.  I will see if there is a more transparent way to  
> enable it, certainly having the SQLite flags be visible in  
> Makevars.in would be an improvement.


> The configure setup for RSQLite is more complicated than I would  
> like because it supports building the included SQLite sources  
> (default) but also linking to an external system SQLite.

Yeah, I noticed you can link to an external sqlite when I was foraging  
through the RSQLite package source, that's very clever.

>> Just to be sure, would it be better/safer to assume (by those of us  
>> who
>> might want to rely on this feature) that it's always compiled this  
>> way
>> if this flag is also set in the src/Makevars.in/PKG_CPPFLAGS line  
>> as well?
> You can rely on the feature without modifying the sources.  I will  
> see if I can improve the transparency of the SQLite config, but  
> there is no plan to remove features (certainly not without good  
> reason and much discussion).


While a more "transparent" configure would be nice, I could understand  
punting on trying to work on that, since I could imagine it being  
quite a burden with little "end-user" appreciation.

>> Lastly, can I humbly appeal to include a more recent version of the
>> sqlite src in the RSQLite package for the future?
>> It looks like the version included is 3.6.4, and we're up to 3.6.19  
>> with
>> a plethora of bug fixes and performance enhancements happening  
>> between
>> the two versions.
> Yes, thanks for the reminder.  A new version of RSQLite is in the  
> works and will include the latest SQLite.


Thanks again,

Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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