[BioC] ArrayExpressHTS fails to load

[Dan Tenenbaum]

Hi Sean,

On Tue, Oct 18, 2011 at 7:45 AM, Sean Rogers <srogers at msu.edu> wrote:
> Hello,
>
> I have recently installed the package ArrayExpressHTS. However it fails
> to load into R. Could someone tell me if this is something I can fix or
> is it perhaps a conflict related to Mac OS X Lion?
>
> Thanks for your help/suggestions.
> Regards
>
> Sean A. Rogers Ph. D.
>
> Research Associate, Department of Horticulture
> Michigan State University
> East Lansing, Michigan USA 48824
>
> library("ArrayExpressHTS")
> Loading required package: sampling
> Loading required package: MASS
> Loading required package: lpSolve
> Loading required package: Rsamtools
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
>    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
>    pmin, pmin.int, rbind, rep.int, setdiff, table, union
>
> Loading required package: GenomicRanges
> Loading required package: Biostrings
> Loading required package: snow
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object
> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/
> ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so':
>  dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/library/
> ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so, 6): Symbol not found: _bam_aux2i
>  Referenced from: /Library/Frameworks/R.framework/Versions/2.13/Resources/library/
> ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so
>  Expected in: dynamic lookup
>
> Error: package/namespace load failed for 'ArrayExpressHTS'
>

It looks like there is a problem with the way this package is built,
there are some build errors here that do not show up as a failure in
our build report:
http://bioconductor.org/checkResults/release/bioc-LATEST/ArrayExpressHTS/pelham-buildbin.html

We will look into this.

In the meantime, you could try:

R --arch i386

The 32-bit version seems to work.

Dan


>
> sessionInfo()
> R version 2.13.2 (2011-09-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/en_US.UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] snow_0.3-7          Rsamtools_1.4.3     Biostrings_2.20.4
> [4] GenomicRanges_1.4.8 IRanges_1.10.6      sampling_2.4
> [7] lpSolve_5.6.6       MASS_7.3-14
>
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.14.1 Biobase_2.12.2       DBI_0.2-5
>  ...
> [25] svMisc_0.9-63        tools_2.13.2         xtable_1.6-0
>
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