Hi Herve,
Thanks for your reply.
I updated my R to yesterday's building and it works great. Looks like it
is the problem of my old version of R 3.10.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 12/13/13 2:50 PM, "Hervé Pagès" <hpa...@fhcrc.org> wrote:
>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 ŒGAlignments¹, ŒGAlignmentPairs¹ 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 * Out-of-date packages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@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
>1100 Fairview Ave. N, M1-B514
>P.O. Box 19024
>Seattle, WA 98109-1024
>
>E-mail: hpa...@fhcrc.org
>Phone: (206) 667-5791
>Fax: (206) 667-1319
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