Cannot install GenomicFeatures package (related to RSQLite version)
1
0
Entering edit mode
vimartin • 0
@vimartin-7105
Last seen 9.3 years ago
France

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

 

 

biocinstaller genomicfeatures rsqlite • 3.2k views
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3
Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.1 years ago
United States

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

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0
Entering edit mode

Thanks that totally did the trick!

I guess I should have check the bioconductor version...

Victorin.

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