[BioC] setting names of GAlignmentsList objects

[Hans-Ulrich Klein]

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)
galist <- GAlignmentsList(one=gal, two=gal)
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'


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