Hi,

i am trying to count bam files on a specific bed file with the following script. Unfortunately, the same snippet, which worked good a only last week, is not running any more.

I keep getting error messages like the one mentioned above, but interestingly only when I call the object, not when I am running the command. When I run this snippet:

chromLength <- seqinfo(Scerevisiae)

# create the Granges obejct with 500 bases width windows
bins1 <- tileGenome(seqinfo(Scerevisiae), tilewidth=500, cut.last.tile.in.chrom=TRUE)
seqlevelsStyle(bins1)

seqlevelsStyle(bins1) <- "NCBI"
# read the bam files into R
Rad51 <- readGAlignments("1.Ensembl.sorted.bam")
In <- readGAlignments("2.Ensembl.sorted.bam")
seqlevelsStyle(In)

it doesn't show any error/warnings

but when I try to call the objects:

> chromLength
Seqinfo object with 17 sequences (1 circular) from sacCer3 genome:
Error in nchar(rownames.label) :
  could not find symbol "keepNA" in environment of the generic function
> Rad51
GAlignments object with 2057068 alignments and 0 metadata columns:
Error in nchar(x, type = "width") :
  could not find symbol "keepNA" in environment of the generic function
> In
GAlignments object with 2099495 alignments and 0 metadata columns:
Error in nchar(x, type = "width") :
  could not find symbol "keepNA" in environment of the generic function

What is happening here?

another problem occurs when I try to run summarizeOverlaps and count the reads on specific regions in a bed file

bamFiles <- list.files(path = "~/Projects/Claudio_ChIPSeq/", pattern = ".bam$", full.names = TRUE)

> bins1
GRanges object with 24322 ranges and 0 metadata columns:
          seqnames         ranges strand
             <Rle>      <IRanges>  <Rle>
      [1]        I   [   1,  500]      *
      [2]        I   [ 501, 1000]      *
      [3]        I   [1001, 1500]      *
      [4]        I   [1501, 2000]      *
      [5]        I   [2001, 2500]      *
      ...      ...            ...    ...
  [24318]       MT [83501, 84000]      *
  [24319]       MT [84001, 84500]      *
  [24320]       MT [84501, 85000]      *
  [24321]       MT [85001, 85500]      *
  [24322]       MT [85501, 85779]      *
  -------
  seqinfo: 17 sequences (1 circular) from sacCer3 genome
> bamFiles
[1] "/Users/ayeroslaviz/Projects/Claudio_ChIPSeq/In.Ensembl.sorted.bam"   
[2] "/Users/ayeroslaviz/Projects/Claudio_ChIPSeq/Rad51.Ensembl.sorted.bam"

but than:

> olapTable <- summarizeOverlaps(bins1, bamFiles, inter.feature=FALSE)
Error in SummarizedExperiment(assays = SimpleList(counts = counts), rowRanges = features,  :
  error in evaluating the argument 'assays' in selecting a method for function 'SummarizedExperiment': Error in validObject(.Object) :
  invalid class “SimpleList” object: invalid object for slot "listData" in class "SimpleList": got class "matrix", should be or extend class "list"

thanks

Assa

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] csaw_1.2.1                              BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0
 [3] BSgenome_1.36.1                         rtracklayer_1.28.5                     
 [5] GenomicAlignments_1.4.1                 Rsamtools_1.20.4                       
 [7] Biostrings_2.36.1                       XVector_0.8.0                          
 [9] GenomicRanges_1.20.5                    GenomeInfoDb_1.4.1                     
[11] IRanges_2.2.5                           S4Vectors_0.6.1                        
[13] BiocGenerics_0.14.0                    

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.30.1   edgeR_3.10.2           zlibbioc_1.14.0        BiocParallel_1.2.6    
 [5] tools_3.2.0            Biobase_2.28.0         DBI_0.3.1              lambda.r_1.1.7        
 [9] futile.logger_1.4.1    futile.options_1.0.0   bitops_1.0-6           biomaRt_2.24.0        
[13] RCurl_1.95-4.7         RSQLite_1.0.0          limma_3.24.12          GenomicFeatures_1.20.1
[17] XML_3.98-1.3         

> RStudio.Version()
$citation

To cite RStudio in publications use:

  RStudio Team (2015). RStudio: Integrated Development for R. RStudio, Inc., Boston, MA URL
  http://www.rstudio.com/.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {RStudio: Integrated Development Environment for R},
    author = {{RStudio Team}},
    organization = {RStudio, Inc.},
    address = {Boston, MA},
    year = {2015},
    url = {http://www.rstudio.com/},
  }

$mode
[1] "desktop"

$version
[1] ‘0.99.447’

solved!

There were some inconsistencies between the new packages and the R base version.

I have updated R to 3.2.1 and now it works again.

I encountered the same error message when I used a script that worked well on one computer and not on a second. Similar to your problem The problem computer is using Biostrings 2.36.1, and the one that works is using Biostrings 2.34.1.

In my case, I got the error when using the function: readDNAStringSet() to read in a fasta file. I'm trying to figure out how to roll back the Biostrings package version to see if this will help. 

Reed

Hi,

I am new in R and I get a similar error:

Error in nchar(x, type = "bytes") : 
  could not find symbol "keepNA" in environment of the generic function

When I try to follow the guideline scipt here: 

http://rstudio-pubs-static.s3.amazonaws.com/12097_1352791b169f423f910d93222a4c2d85.html

I tried to install an older version of the package, but this was not possible, error:

Warning message:
package ‘Biostrings_2.30.1’ is not available (for R version 3.2.0) 

I really would like to get this command to work, I haven't been able to find another (updated) R-script on the web, so if anyone knows what I need to do, I will be very happy to hear from you.

Best wishes,

Mathilde