[BioC] pileupAsGranges invalid times error

[Katherine Yahvah]

Hello-
I'm running into an almost identical problem that was previously posted (
https://stat.ethz.ch/pipermail/bioconductor/2013-March/051793.html ) but
have not found a solution to make the analysis work.

I am trying to use pileupAsGRanges to generate the base counts at each
nucleotide position in a GRanges object.  My GRanges object:
> gr
GRanges with 225 ranges and 1 metadata column:
        seqnames               ranges strand   |   seqinfo
           <Rle>            <IRanges>  <Rle>   | <integer>
    [1]     chr1 [ 4367322,  4367323]      *   |         1
    [2]     chr1 [14155401, 14155402]      *   |         2
    [3]     chr1 [14996653, 14996654]      *   |         3
    [4]     chr1 [34155500, 34155501]      *   |         4
    [5]     chr1 [54195017, 54195018]      *   |         5
    ...      ...                  ...    ... ...       ...
  [221]    chr22 [43579707, 43579708]      *   |       221
  [222]    chr22 [47836411, 47836412]      *   |       222
  [223]    chr22 [48362289, 48362290]      *   |       223
  [224]     chrY [ 8619537,  8619538]      *   |       224
  [225]     chrY [14096576, 14096577]      *   |       225
  ---
  seqlengths:
    chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19  chr2
chr20 chr21 chr22  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chrY
      NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA
NA    NA    NA    NA    NA    NA    NA    NA    NA    NA    NA


However, when I try to run pileupAsGRanges I get an error:

>
test<-pileupAsGRanges(bam=fls,regions=gr,maxDepth=.Machine$integer.max,minBa
seQuality=30, minMapQuality=30)
Error: applyPileups: invalid 'times' argument
In addition: Warning messages:
1: In start(regions):end(regions) :
  numerical expression has 225 elements: only the first used
2: In start(regions):end(regions) :
  numerical expression has 225 elements: only the first used

If I run the command with only one element of the GRanges object the
function works:

>
test<-pileupAsGRanges(bam=fls,regions=gr[1],maxDepth=.Machine$integer.max,mi
nBaseQuality=30, minMapQuality=30)
> test
GRanges with 2 ranges and 7 metadata columns:
      seqnames             ranges strand |         A         C         G
T         N     depth                        bam
         <Rle>          <IRanges>  <Rle> | <integer> <integer> <integer>
<integer> <integer> <numeric>                <character>
  [1]     chr1 [4367322, 4367322]      + |       233         0         1
0         0       234 ./IonXpress_001_rawlib.bam
  [2]     chr1 [4367323, 4367323]      + |       467         0         0
0         0       467 ./IonXpress_001_rawlib.bam
  ---
  seqlengths:
   chr1
     NA

Any help to figure out how to correct or work around this problem would be
greatly appreciated.
Regards,
Katherine Yahvah
Research Scientist
Kashi Clinical Laboratories
Portland, OR

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United
States.1252    

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets
methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19  ChIPpeakAnno_2.10.0
GenomicFeatures_1.14.3             
 [4] limma_3.18.13                       org.Hs.eg.db_2.10.1
GO.db_2.10.1                       
 [7] RSQLite_0.11.4                      DBI_0.2-7
AnnotationDbi_1.24.0               
[10] BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.30.0
multtest_2.18.0                    
[13] Biobase_2.22.0                      biomaRt_2.18.0
VennDiagram_1.6.5                  
[16] Rsamtools_1.14.3                    Biostrings_2.30.1
biovizBase_1.10.7                  
[19] BiocInstaller_1.12.0                GenomicRanges_1.14.4
XVector_0.2.0                      
[22] IRanges_1.20.6                      BiocGenerics_0.8.0                 

loaded via a namespace (and not attached):
 [1] bitops_1.0-6        cluster_1.14.4      colorspace_1.2-4
dichromat_2.0-0     Formula_1.1-1       Hmisc_3.14-1        labeling_0.2

 [8] lattice_0.20-24     latticeExtra_0.6-26 MASS_7.3-29
munsell_0.4.2       plyr_1.8            RColorBrewer_1.0-5  RCurl_1.95-4.1

[15] rtracklayer_1.22.3  scales_0.2.3        splines_3.0.2
stats4_3.0.2        stringr_0.6.2       survival_2.37-7     tools_3.0.2

[22] XML_3.98-1.1        zlibbioc_1.8.0