[BioC] setting names of GAlignmentsList objects

[Martin Morgan]

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
>
>


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