[Debian-med-packaging] [devteam-bioc] Error when running test suite of GenomicAlignments

[Dan Tenenbaum]

----- Original Message -----
> From: "Maintainer" <maintainer at bioconductor.org>
> To: "Bioconductor Package Maintainer" <maintainer at bioconductor.org>
> Cc: "Debian Med Packaging Team" <debian-med-packaging at lists.alioth.debian.org>
> Sent: Friday, June 26, 2015 10:25:55 PM
> Subject: [devteam-bioc] Error when running test suite of GenomicAlignments
> 
> Hi,
> 
> as you might remember the Debian Med team is packaging several
> BioConductor tools.  When running the according test suite via
> 
> LC_ALL=C R --no-save <<EOT
> BiocGenerics:::testPackage("GenomicAlignments")
> EOT
> 
> I get
> 
> ...
> [samopen] SAM header is present: 3 sequences.
> Timing stopped at: 0.148 0.004 0.152
> Error : objects 'DataFrame', 'isSingleString', 'isTRUEorFALSE',
> 'SimpleList' are not exported by 'namespace:IRanges'
> 
> 
> RUNIT TEST PROTOCOL -- Sat Jun 27 07:19:26 2015
> ***********************************************
> Number of test functions: 33
> Number of errors: 1
> Number of failures: 0
> 
> 
> 1 Test Suite :
> GenomicAlignments RUnit Tests - 33 test functions, 1 error, 0
> failures
> ERROR in test_readGAlignments_BamViews: Error : objects 'DataFrame',
> 'isSingleString', 'isTRUEorFALSE', 'SimpleList' are not exported by
> 'namespace:IRanges'
> 
> Test files with failing tests
> 
>    test_readGAlignments.R
>      test_readGAlignments_BamViews
> ...
> 
> I made sure that I'm using the latest IRanges 2.2.4.
> 
> Any hint what might have done wrong?
> 

Please send us your sessionInfo() after loading GenomicAlignments. You might also try
BiocInstaller::biocValid()

Dan


> Kind regards and thanks for providing BioConductor
> 
>     Andreas.
> 
> --
> http://fam-tille.de
> 
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