[Bioc-devel] GenomicFeatures Install Fails

[Dario Strbenac]

Thanks. It installed this time. One of those packages was out of date in my library.

---- Original message ----
>Date: Sun, 10 Apr 2011 23:10:11 -0700
>From: Hervé Pagès <hpages at fhcrc.org>  
>Subject: Re: [Bioc-devel] GenomicFeatures Install Fails  
>To: Wei Shi <shi at wehi.EDU.AU>
>Cc: D.Strbenac at garvan.org.au, bioc-devel at r-project.org
>
>Hi Dario, Wei,
>
>Remember that this is devel and some packages might introduce changes
>that affect other packages. So please make sure that you update
>your installation frequently:
>
>   source("http://bioconductor.org/biocLite.R")
>   update.packages(repos=biocinstallRepos(), ask=FALSE, checkBuilt=TRUE)
>
>For the particular problem you are seeing, make sure you have the
>latest versions of IRanges, GenomicRanges, Biostrings, BSgenome,
>and rtracklayer before you try to install GenomicFeatures.
>
>Cheers,
>H.
>
>
>On 11-04-10 09:04 PM, Wei Shi wrote:
>> I got that problem too ...
>>
>> Wei
>>
>> On Apr 11, 2011, at 2:00 PM, Dario Strbenac wrote:
>>
>>> Hello,
>>>
>>> I'm having problems installing the package GenomicFeatures, development version. I've looked at http://www.bioconductor.org/checkResults/2.8/bioc-LATEST/ and it doesn't have warnings or errors there, but when I try to install it I get :
>>>
>>> * installing *source* package âGenomicFeaturesâ ...
>>>   ...          ...
>>> Error : class "Sequence" is not exported by 'namespace:IRanges'
>>> ERROR: lazy loading failed for package âGenomicFeaturesâ
>>>   ...          ...
>>>
>>> I've got the latest IRanges installed though.
>>>> library(IRanges)
>>>   ...          ...
>>>> sessionInfo()
>>> R version 2.13.0 RC (2011-04-05 r55310)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>   ...         ...
>>> other attached packages:
>>> [1] IRanges_1.9.31
>>>   ...         ...
>>>
>>> Am I doing something wrong, or are there some more changes to be made before it goes to release ?
>>>
>>> --------------------------------------
>>> Dario Strbenac
>>> Research Assistant
>>> Cancer Epigenetics
>>> Garvan Institute of Medical Research
>>> Darlinghurst NSW 2010
>>> Australia
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> ______________________________________________________________________
>> The information in this email is confidential and intend...{{dropped:6}}
>>
>> _______________________________________________
>> 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
>1100 Fairview Ave. N, M2-B876
>P.O. Box 19024
>Seattle, WA 98109-1024
>
>E-mail: hpages at fhcrc.org
>Phone:  (206) 667-5791
>Fax:    (206) 667-1319


--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia