Dear List,

I have some problem loading DESeq after I upgraded from R 2.14 to R .2.15 on Mac OS 10.7.3. 

Basically, I have my own library directory separate from the default library directory (/Library/Frameworks/R.framework/Versions/2.14/Resources/library) to avoid having to re-instally all the packages after changing from 2.14 to 2.15. I also set up my .libPaths("/Library/RLib") in the ~/.Rprofile and R_LIBS=/Library/RLib in my .profile at $HOME.

After that, I installed the binary build R 2.15 and upgraded all packages.

Under terminal window, I can load all of the packages including DESeq and DEXSeq.  Under R64.app GUI, however, I can load all packages except for DESeq and DEXSeq in R GUI.

Please anyone has some suggestions?

Thanks very much!


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Under terminal:
> library(DESeq)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: locfit
locfit 1.5-7 	 2012-03-22
> 


################################################################################


Under R64 or R32 GUI:

> library(DESeq)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map,
    mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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’






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