[BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
Taylor, Sean D
sdtaylor at fhcrc.org
Thu Feb 28 23:51:58 CET 2013
Yes, strange indeed. I just tried uninstalling everything I could think of and reinstalling R 3.0 and RStudio from the RStudio 0.97.318 installer. Still no luck. I will take your other suggestion and post to the RStudio forums.
Thanks,
Sean
-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
Sent: Thursday, February 28, 2013 2:41 PM
To: Taylor, Sean D
Cc: Sean [guest]; bioconductor at r-project.org
Subject: Re: [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
On Thu, Feb 28, 2013 at 2:33 PM, Taylor, Sean D <sdtaylor at fhcrc.org> wrote:
> Hi Dan,
>
> Thanks for the biocLite tip, that seems to have gotten me past that particular hurdle.
>
> For the RStudio issue, I am running Windows 7, 64-bit. I will append my sessionInfo() again at the end. I had a previous version of R on this machine, 2.15.1. I tried installing the R-devel in parallel, but when that wasn't working I uninstalled it. Now I just have the R-devel version. To open RStudio, I have tried holding down the Ctrl key while opening. Here I have the option of selecting the 32-bit or the 64-bit version of R-devel. I have tried both with the same result, i.e. fatal error. Is there a way of checking to see if there is still some part of the previous version that is getting in the way?
>
At this point I think your best bet is to report the issue on RStudio's forums:
http://support.rstudio.org/
> Thanks
> Sean
>
>> sessionInfo()
> R Under development (unstable) (2013-02-21 r62017)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.19 BSgenome_1.27.1
> [3] BiocInstaller_1.9.6 Biostrings_2.27.11
> [5] IntermediateSequenceAnalysis2013_0.1.1 SequenceAnalysisData_0.1.4
> [7] edgeR_3.1.4 limma_3.15.14
> [9] GenomicFeatures_1.11.11 AnnotationDbi_1.21.10
> [11] Biobase_2.19.2 GenomicRanges_1.11.30
> [13] IRanges_1.17.35 BiocGenerics_0.5.6
>
> loaded via a namespace (and not attached):
> Error in x[["Version"]] : subscript out of bounds In addition: Warning
> message:
> In FUN(c("biomaRt", "bitops", "DBI", "RCurl", "Rsamtools", "RSQLite", :
> DESCRIPTION file of package 'Rsamtools' is missing or broken
>>
This is rather strange, though....this should not be happening.
I might suggest completely removing your R installation and starting again from scratch, if that is practical.
Dan
>
>
>
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
> Sent: Thursday, February 28, 2013 1:46 PM
> To: Sean [guest]
> Cc: bioconductor at r-project.org; Taylor, Sean D
> Subject: Re: [BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
>
> Hi Sean,
>
>
> On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest at bioconductor.org> wrote:
>>
>> I am trying to get myself more familiar with Bioconductor, so I have been walking through the vignette of the 2013 Intermediate R/Bioconductor for Sequence Analysis course offered earlier this month (February 2013). (Link to course page and vignette: http://www.bioconductor.org/help/course-materials/2013/SeattleFeb2013/).
>>
>> I have installed R 3.0 and Bioconductor 2.12 as per the instructions in the vignette. I now have two problems:
>>
>> The first seems relatively minor: I cannot seem to get RStudio to open R 3.0. I simply get a message that says that "The R session had a fatal error." I can open R using its own GUI, but it would be nice to work within RStudio.
>>
>> The second is a bit more problematic. I have been able to follow the
>> vignette without too many problems up until Chapter 5 "Strings and Reads". The exercise has you load the BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download the package using the provided link to the development version of the Drosophila genome (http://bioconductor.org/packages/devel/data/annotation/html/BSgenome.Dmelanogaster.UCSC.dm3.html) and by entering the following code:
>>
>>>source("http://bioconductor.org/biocLite.R")
>>>biocLite("BSgenome.Dmelanogaster.UCSC.dm3")
>>
>> However, when I try to load the library, I get the following:
>>
>>> library(BSgenome.Dmelanogaster.UCSC.dm3)
>> Error: package ‘BSgenome.Dmelanogaster.UCSC.dm3’ was built before
>> R 3.0.0: please re-install it
>>
>> The library installs on earlier releases of R, but I cannot convince it to run on R 3.0 where I can make use of the current vignette.
>>
>> Any advice on either of these two issues, but particularly the second, would be greatly appreciated.
>>
>
> Try this:
> biocLite("BSgenome.Dmelanogaster.UCSC.dm3", type="source")
>
> As for RStudio, I'm not sure, what is your OS and output of sessionInfo()? I successfully use RStudio with R-3.0.0. Make sure that the first R in your path is R-devel.
>
> Dan
>
>
>> Sean
>>
>> -- output of sessionInfo():
>>
>>> sessionInfo()
>> R Under development (unstable) (2013-02-21 r62017)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United
>> States.1252 [3] LC_MONETARY=English_United States.1252 [4]
>> LC_NUMERIC=C [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] parallel stats graphics grDevices utils datasets methods
>> [8] base
>>
>> other attached packages:
>> [1] Biostrings_2.27.11
>> [2] IntermediateSequenceAnalysis2013_0.1.1
>> [3] SequenceAnalysisData_0.1.4
>> [4] edgeR_3.1.4
>> [5] limma_3.15.14
>> [6] GenomicFeatures_1.11.11
>> [7] AnnotationDbi_1.21.10
>> [8] Biobase_2.19.2
>> [9] GenomicRanges_1.11.30
>> [10] IRanges_1.17.35
>> [11] BiocGenerics_0.5.6
>>
>> loaded via a namespace (and not attached):
>> [1] biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5
>> [5] RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 rtracklayer_1.19.9
>> [9] stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 zlibbioc_1.5.0
>>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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