[Bioc-devel] GenomicFeatures on 2.13.1 Windows

[Hervé Pagès]

On 11-08-01 08:00 PM, Dario Strbenac wrote:
> I made sure it's the release version by looking at the DESCRIPTION file of GenomicFeatures folder in the first library path given by .libPaths(), and it is because it's version 1.4.4. Is there something else I should try ?

Ah ok. Well I'm not sure what's going on exactly. Seems like you have
a stalled package somewhere. I would suggest you try to re-install at
least IRanges, GenomicRanges, rtracklayer, Biostrings, BSgenome and
GenomicFeatures with biocLite(). See if that helps. Let us know if the
problem persists after this.

Cheers,
H.

>
> ---- Original message ----
>> Date: Mon, 01 Aug 2011 18:01:51 -0700
>> From: Hervé Pagès<hpages at fhcrc.org>
>> Subject: Re: [Bioc-devel] GenomicFeatures on 2.13.1 Windows
>> To: D.Strbenac at garvan.org.au
>> Cc: bioc-devel at r-project.org
>>
>> Hi Dario,
>>
>> Seems like you are trying to use the devel version of GenomicFeatures
>> with BioC release. Not a good idea...
>>
>> Cheers,
>> H.
>>
>>
>> On 11-07-28 08:00 PM, Dario Strbenac wrote:
>>> Hello,
>>>
>>> I'm having some troubles loading GenomicFeatures. I'm on a Windows 7 64 bit PC. This is the output I see, in a new session of R.
>>>
>>>> library(GenomicFeatures)
>>> Loading required package: IRanges
>>>
>>> Attaching package: 'IRanges'
>>>
>>> The following object(s) are masked from 'package:base':
>>>
>>>       cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union
>>>
>>> Loading required package: GenomicRanges
>>> Error : class "Sequence" is not exported by 'namespace:IRanges'
>>> Error: package/namespace load failed for 'GenomicFeatures'
>>>> sessionInfo()
>>> R version 2.13.1 (2011-07-08)
>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
>>> [5] LC_TIME=English_Australia.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] GenomicRanges_1.4.6 IRanges_1.10.4
>>>
>>> loaded via a namespace (and not attached):
>>> [1] biomaRt_2.6.0     Biostrings_2.20.1 BSgenome_1.20.0   DBI_0.2-5         RCurl_1.5-0.1     RSQLite_0.9-4     XML_3.2-0.2
>>>> GRanges()
>>> GRanges with 0 ranges and 0 elementMetadata values
>>>        seqnames ranges strand |
>>>
>>> seqlengths
>>>
>>>
>>>> IRanges()
>>> IRanges of length 0
>>>
>>> Strangely, GenomicRanges seems to have been loaded, although the loading gave an error message.
>>>
>>> In another new R session, I can load GenomicRanges just fine.
>>>
>>>> library(GenomicRanges)
>>> Loading required package: IRanges
>>>
>>> Attaching package: 'IRanges'
>>>
>>> The following object(s) are masked from 'package:base':
>>>
>>>       cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int,
>>>       pmin, pmin.int, rbind, rep.int, setdiff, table, union
>>>
>>>> sessionInfo()
>>> R version 2.13.1 (2011-07-08)
>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
>>> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
>>> [5] LC_TIME=English_Australia.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] GenomicRanges_1.4.6 IRanges_1.10.4
>>>
>>> Does anyone else have the same problem ?
>>>
>>> --------------------------------------
>>> 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
>>
>>
>> --
>> 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: 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


-- 
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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319