[BioC] problem with loading DESeq after upgrading from R 2.14 to R 2.15

[Steve Lianoglou]

Hi,

The way you are trying to maintain your libraries is generally frowned
upon. You shouldn't be trying to use R-2.14 packages with your R-2.14
install. You are exposing yourself to weird and hard to explain
problems.

Look at the error message you are getting:

On Mon, Apr 23, 2012 at 3:36 PM, Yue Li <yueli at cs.toronto.edu> wrote:
[snip]
> Loading required package: locfit
> locfit 1.5-7     2012-03-22
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object '/Library/RLib/RSQLite/libs/x86_64/RSQLite.so':
>  dlopen(/Library/RLib/RSQLite/libs/x86_64/RSQLite.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib
>  Referenced from: /Library/RLib/RSQLite/libs/x86_64/RSQLite.so
>  Reason: image not found
> Error: package/namespace load failed for ‘DESeq’

Your trying to load a package from your 2.14 repo ... I'm not sure why
this works from the terminal and not the GUI (are you sure you are
firing up 2.15 from the terminal?), but I'm also not too inclined to
smoke this out, because ... well, you shouldn't be doing this ;-) and
also it will likely take you less time to just install things "the
normal way".

If you really have some compelling reason to have a custom library
structure, I like the way the bioc folks suggest developers to keep
bioc-devel package separate from bioc-release (now that R is on an
annual release cycle), eg:

http://www.bioconductor.org/developers/useDevel/

You could imagine having R-2.14 and R-2.15 in separate dirs instead of
2.15-release and 2.15-devel if working w/ devel libraries isn't your
cup of tea -- but note they still keep different versions different.

Anyway, the "normal" R install does this for you anyway on OS X, so
dollars-to-donuts you'll have less hassles just going "the normal"
route, and installing the package you need via biocLite again in your
"clean" 2.15 library path will likely cost less time than trying to
debug your custom library path woes.

HTH,
-steve


-- 
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