[Bioc-devel] error when install ŒRsamtools¹, ŒGenomicAlignments¹ and Œrtracklayer¹

[Hervé Pagès]

Hi Jianhong,

On 12/13/2013 11:45 AM, Ou, Jianhong wrote:
> Dear all,
>
> When I try to renew Rsamtools, GenomicAlignments and rtracklayer, I got error
>
> Error : objects ‘GAlignments’, ‘GAlignmentPairs’ are not exported by 'namespace:GenomicRanges'

You didn't show us what you did exactly.

Try to do:

   biocLite("GenomicRanges")
   biocLite("Rsamtools")
   biocLite("GenomicAlignments")
   biocLite("rtracklayer")
   biocLite()

in *that* order.

Cheers,
H.

>
> Does anybody know how to figure out this problem?
>
>> biocValid()
>
> * sessionInfo()
>
> R Under development (unstable) (2013-09-29 r64014)
> Platform: x86_64-apple-darwin12.5.0 (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] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.13.3                      TxDb.Mmusculus.UCSC.mm10.knownGene_2.10.1
> [3] GenomicFeatures_1.15.4                    AnnotationDbi_1.25.9
> [5] Biobase_2.23.3                            GenomicRanges_1.15.13
> [7] XVector_0.3.3                             IRanges_1.21.14
> [9] BiocGenerics_0.9.1
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.19.1           Biostrings_2.31.3        bitops_1.0-6
>   [4] BSgenome_1.31.7          DBI_0.2-7                GenomicAlignments_0.99.3
>   [7] RCurl_1.95-4.1           Rsamtools_1.15.9         RSQLite_0.11.4
> [10] rtracklayer_1.23.3       stats4_3.1.0             tools_3.1.0
> [13] XML_3.98-1.1             zlibbioc_1.9.0
>
> * Out-of-date packages
>                    Package
> GenomicAlignments "GenomicAlignments"
> Rsamtools         "Rsamtools"
> rtracklayer       "rtracklayer"
>                    LibPath                                                          Installed Built
> GenomicAlignments "/Library/Frameworks/R.framework/Versions/3.1/Resources/library" "0.99.3"  "3.1.0"
> Rsamtools         "/Library/Frameworks/R.framework/Versions/3.1/Resources/library" "1.15.9"  "3.1.0"
> rtracklayer       "/Library/Frameworks/R.framework/Versions/3.1/Resources/library" "1.23.3"  "3.1.0"
>                    ReposVer  Repository
> GenomicAlignments "0.99.9"  "http://bioconductor.org/packages/2.14/bioc/src/contrib"
> Rsamtools         "1.15.15" "http://bioconductor.org/packages/2.14/bioc/src/contrib"
> rtracklayer       "1.23.6"  "http://bioconductor.org/packages/2.14/bioc/src/contrib"
>
> update with biocLite()
>
> Error: 3 package(s) out of date
>
> Yours sincerely,
>
> Jianhong Ou
>
> LRB 670A
> Program in Gene Function and Expression
> 364 Plantation Street Worcester,
> MA 01605
>
> 	[[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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