[BioC] setting names of GAlignmentsList objects

[Hans-Ulrich Klein]

Dear Martin,

yes, it is going nicely in the current release.

I pasted the sessionInfo() but did not look at it :/  Sorry.

Best,
Hans


On 31/10/13 12:45, Martin Morgan wrote:
> On 10/31/2013 02:53 AM, Hans-Ulrich Klein wrote:
>> Dear all,
>>
>> I can not change the list element names of my GAlignmentsList objects:
>>
>> library(GenomicRanges)
>> library(Rsamtools)
>> ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
>> ga <- readGappedAlignments(ex1_file)
>
> The name of this function was changed to readGAlignments in the 
> current version of Bioconcductor
>
>> galist <- GAlignmentsList(one=gal, two=gal)
>
> oops, one=ga, two=ga
>
>> names(galist)
>>
>> names(galist) <- c("three", "four")
>> Error in `names<-`(`*tmp*`, value = c("three", "four")) :
>>    replacement 'value' is not an AtomicList with the same 
>> elementLengths as 'x'
>>
>> names(galist) <- names(galist)
>> Error in `names<-`(`*tmp*`, value = c("one", "two")) :
>>    replacement 'value' is not an AtomicList with the same 
>> elementLengths as 'x'
>
> this works in the current release; try
>
>   biocLite("BiocUpgrade")
>
> and get (other than the R version)
>
> > sessionInfo()
> R version 3.0.2 Patched (2013-10-02 r64018)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets methods
> [8] base
>
> other attached packages:
> [1] Rsamtools_1.14.1     Biostrings_2.30.0    GenomicRanges_1.14.3
> [4] XVector_0.2.0        IRanges_1.20.4       BiocGenerics_0.8.0
> [7] BiocInstaller_1.12.0
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-6   stats4_3.0.2   zlibbioc_1.8.0
>
>>
>>
>> Any ideas what is going wrong?
>>
>> Thanks and best wishes,
>> Hans
>>
>>
>>  > sessionInfo()
>> R version 3.0.1 (2013-05-16)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=C                 LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets methods
>> [8] base
>>
>> other attached packages:
>> [1] Rsamtools_1.12.4     Biostrings_2.28.0 GenomicRanges_1.12.5
>> [4] IRanges_1.18.4       BiocGenerics_0.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] bitops_1.0-6   stats4_3.0.1   tools_3.0.1    zlibbioc_1.6.0
>>
>>
>
>


-- 
Dr. Hans-Ulrich Klein
Institute of Medical Informatics
University of Münster
Albert-Schweitzer-Campus 1
Gebäude A11
48149 Münster, Germany
Tel.: +49 (0)251 83-58405