Looks like there is some mix & matching going on? (mentioning this because
it seems intriguing - for me - the fact that you're running R-2.15.2, but
the error also refers to R.framework/Versions/2.13)

Note that the package that is failing is 'bit' (which is not a BioC
package), so reinstall it (the failure is because R cannot find the 64-bit
image of that package) and its friends (the ff package). Also allow
BiocInstaller to update your existing packages. Although they're not a BioC
packages, you can use biocLite() for the task:

> biocLite(c('bit', 'ff'))
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'bit' 'ff'
trying URL '
http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/bit_1.1-9.tgz'
Content type 'application/x-gzip' length 223228 bytes (217 Kb)
opened URL
==================================================
downloaded 217 Kb

trying URL '
http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/ff_2.2-10.tgz'
Content type 'application/x-gzip' length 1629830 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb


Regarding the error with the installation of RSQLite, I can't reproduce the
issue:

> biocLite("RSQLite")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'RSQLite'
trying URL '
http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15/RSQLite_0.11.2.tgz'
Content type 'application/x-gzip' length 2219524 bytes (2.1 Mb)
opened URL
==================================================
downloaded 2.1 Mb
> sessionInfo()
R version 2.15.2 RC (2012-10-25 r61014)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] tools_2.15.2



On 16 November 2012 15:12, YBao <yb8d@virginia.edu> wrote:

> Hi All,
>
> I recently updated my R to 2.15.2 and reloaded the bioc packages. Then I
> started to have troubles making use of a number of packages, not the least
> with OLIGO which I have been using frequently before this updating. Can
> someone in the know lend a helping hand on this. Below is the error message
>
> > library(oligo)
> Loading required package: oligoClasses
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared object
> '/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so':
>   dlopen(/Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so, 6):
> Library not loaded:
> /Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib
>   Referenced from:
> /Users/yb8d/Library/R/2.15/library/bit/libs/x86_64/bit.so
>   Reason: image not found
> Error: package ‘oligoClasses’ could not be loaded
>
> Then when I tried to load RSQLite I got this error:
> > biocLite("RSQLite")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'RSQLite'
> Warning: unable to access index for repository
> http://software.rc.fas.harvard.edu/mirrors/R/src/contrib
> Warning: unable to access index for repository
>
> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contrib/2.15
> Warning: unable to access index for repository
>
> http://software.rc.fas.harvard.edu/mirrors/R/bin/macosx/leopard/contrib/2.15
> Warning message:
> package ‘RSQLite’ is not available (for R version 2.15.2)
>
> And my sessionInfo:
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] BiocInstaller_1.8.3   ALL_1.4.13            RColorBrewer_1.0-2
>  lattice_0.20-10       limma_3.14.1          affyPLM_1.34.0
>  preprocessCore_1.20.0
>  [8] gcrma_2.30.0          affydata_1.11.17      affy_1.36.0
> Biobase_2.18.0        BiocGenerics_0.4.0    R.utils_1.7.5
> R.oo_1.8.0
> [15] R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.26.0        Biostrings_2.26.2    DBI_0.2-5
>  GenomicRanges_1.10.5 grid_2.15.2          IRanges_1.16.4
> parallel_2.15.2
>  [8] splines_2.15.2       stats4_2.15.2        tools_2.15.2
> xtable_1.5-6         zlibbioc_1.4.0
>
> Best,
>
> Yongde
>
>
> --
> Yongde Bao
> Dept. of Microbiology, Immunology,
>              and Cancer Biology
> UVA
>
>         [[alternative HTML version deleted]]
>
>
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