[BioC] ArrayExpressHTS fails to load

[Martin Morgan]

On 10/19/2011 10:30 PM, Dan Tenenbaum wrote:
> 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.

or (untested) build packages Rsamtools and ArrayExpressHTS from source. 
Martin

>
> 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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>
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