[Bioc-sig-seq] GenomicFeatures package

Seth Falcon sfalcon at fhcrc.org
Mon Nov 2 17:52:55 CET 2009

Hi Steve,

On 11/2/09 8:34 AM, Steve Lianoglou wrote:
> <snipped working example>
> Wow .. I didn't even check to see if it compiles like that be default,
> that's great.
> I assumed that since it *doesn't* compile by default in the sqlite
> distro, I expected it to not do so in the RSQLite install since
> "-DSQLITE_ENABLE_RTREE=1" wasn't added to the src/Makevars.in
> PKG_CPPFLAGS entry, which is currently:
> But searching the package source again, I see that it is defined
> somewhere deep in the configure file. I'm not sure what codepath has to
> be "active" to land in the particular `if` block that that sets
> -DSQLITE_ENABLE_RTREE=1 (my shell scripting mojo is quite weak).

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.

> 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 

> 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.

+ seth

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