Hi Vincent, Is there a reason you've installed it this way, as opposed to biocLite().  I notice you have a mix of release and devel packages in your sessionInfo.  Nevertheless, I get the loading error using --clean and --preclean from the command line. Below, I've reproduced the error on Mac OSX and have loaded IRanges manually to display the version for this dependency:

Rob

> biocLite("Biostrings", type="source")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.9.4), R version 2.16.0.
Installing package(s) 'Biostrings'

<SNIP>

*** installing help indices
** building package indices
** installing vignettes
   'Biostrings2Classes.Rnw' 
   'MultipleAlignments.Rnw' 
   'PairwiseAlignments.Rnw' 
   'matchprobes.Rnw' 
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/libs/x86_64/Biostrings.so':
  dlopen(/Users/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/libs/x86_64/Biostrings.so, 6): Symbol not found: _rcont2
  Referenced from: /Users/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/libs/x86_64/Biostrings.so
  Expected in: flat namespace
 in /Users/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/libs/x86_64/Biostrings.so
Error: loading failed

> library(IRanges)
> sessionInfo()

R Under development (unstable) (2012-10-21 r60988)
Platform: x86_64-apple-darwin12.2.0/x86_64 (64-bit)

locale:
[1] en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII

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

other attached packages:
[1] IRanges_1.17.6      BiocGenerics_0.5.0  BiocInstaller_1.9.4

loaded via a namespace (and not attached):
[1] parallel_2.16.0 stats4_2.16.0   tools_2.16.0   


On Oct 23, 2012, at 9:23 AM, Vincent Carey <stvjc@channing.harvard.edu> wrote:

> can't confirm on either linux or macosx with Oct 23 R-devel build
> 
> Here installed Biostrings from source folder with --clean --preclean
> 
> > library(Biostrings)
> Loading required package: BiocGenerics
> 
> Attaching package: 'BiocGenerics'
> 
> The following object is masked from 'package:stats':
> 
>     xtabs
> 
> The following objects 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
> 
> Loading required package: IRanges
> sessionI> sessionInfo()
> R Under development (unstable) (2012-10-23 r61000)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.ISO8859-1      LC_NUMERIC=C                 
>  [3] LC_TIME=en_US.ISO8859-1       LC_COLLATE=en_US.ISO8859-1   
>  [5] LC_MONETARY=en_US.ISO8859-1   LC_MESSAGES=C                
>  [7] LC_PAPER=C                    LC_NAME=C                    
>  [9] LC_ADDRESS=C                  LC_TELEPHONE=C               
> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C          
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  tools     utils     methods  
> [8] base     
> 
> other attached packages:
> [1] Biostrings_2.27.3   IRanges_1.16.3      BiocGenerics_0.4.0 
> [4] weaver_1.24.0       codetools_0.2-8     digest_0.5.2       
> [7] BiocInstaller_1.8.2
> 
> loaded via a namespace (and not attached):
> [1] parallel_2.16.0 stats4_2.16.0  
> 
> 
> On Tue, Oct 23, 2012 at 7:27 AM, Robert Scharpf <rscharpf@jhsph.edu> wrote:
> Hello,
> 
> I'm having trouble loading the Biostrings package (the Biostrings.so shared library) after installation of the most recent R-devel (Oct 22).  There is no error on the BioC build report, but BioC is building packages from the Oct 5 R-devel.
> 
> Thanks,
> 
> Rob
> 
> biocLite("Biostrings", type="source")
> [...]
> 
> *** installing help indices
> ** building package indices
> ** installing vignettes
>    'Biostrings2Classes.Rnw'
>    'MultipleAlignments.Rnw'
>    'PairwiseAlignments.Rnw'
>    'matchprobes.Rnw'
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared object '/home/bst/student/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/libs/Biostrings.so':
>   /home/bst/student/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/libs/Biostrings.so: undefined symbol: rcont2
> Error: loading failed
> 
> Session info:
> 
> R Under development (unstable) (2012-10-22 r60997)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>  [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>  [7] LC_PAPER=C                     LC_NAME=C
>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
> 
> other attached packages:
> [1] BiocInstaller_1.9.4
> 
> loaded via a namespace (and not attached):
> [1] tools_2.16.0
> 
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 


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