Hi,

I'm trying to install GenomicFeatures through bioconductor (in fact, I'm really trying to install the package "SplicingGraphs" but it fails due to GenomicFeatures). And I have the following error that I failed to understand and, pGenomicFeatureserhaps more importantly, to solve. It seems there is something wrong with the RSQLite (namespace) version (require >=1.0.0) while 0.11.4 is loaded. However as the sessionInfo below shows the RSQLite version installed is 1.0.0.

I've tried to remove and install again RSQLite without any success, I'll be happy to have any suggestion from you.

Thanks.

biocLite("GenomicFeatures",lib.loc="~/R/x86_64-pc-linux-gnu-library/3.1/")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.3), R version
  3.1.2.
Installing package(s) 'GenomicFeatures'
trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicFeatures_1.16.3.tar.gz'
Content type 'application/x-gzip' length 765795 bytes (747 Kb)
opened URL
==================================================
downloaded 747 Kb

* installing *source* package ‘GenomicFeatures’ ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  namespace ‘RSQLite’ 0.11.4 is already loaded, but >= 1.0.0 is required
ERROR: lazy loading failed for package ‘GenomicFeatures’
* removing ‘/home/vmartin/R/x86_64-pc-linux-gnu-library/3.1/GenomicFeatures’

And the sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:GenomicFeatures
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] RSQLite_1.0.0        DBI_0.3.1            BiocInstaller_1.14.3

loaded via a namespace (and not attached):
[1] tcltk_3.1.2 tools_3.1.2

You should really upgrade to Bioconductor 3.0, which has been extensively modified to work with RSQLite 1.0.0.

To upgrade, type

biocLite("BiocUpgrade")

After upgrading, run:

biocLite()

To upgrade all installed packages.

Dan