Hi All,

I'm wondering why the code below throws an error. I'm using R-devel (3.3.0) + BioC-devel. Is this a bug or did I miss something.

From the GenomicAlignments help:

## With a BamViews object:
fls <- system.file("extdata", "ex1.bam", package="Rsamtools",
                    mustWork=TRUE)
bv <- BamViews(fls,
               bamSamples=DataFrame(info="test", row.names="ex1"),
               auto.range=TRUE)
## Note that the "readGAlignments" method for BamViews objects
## requires the ShortRead package to be installed.
aln <- readGAlignments(bv)
Error in readGAlignments(bv) : 
  Assertion on 'more.args' failed: Vector must be named
> sessionInfo()
R Under development (unstable) (2015-07-07 r68639)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)
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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] GenomicAlignments_1.5.11   Rsamtools_1.21.13         
 [3] Biostrings_2.37.2          XVector_0.9.1             
 [5] SummarizedExperiment_0.3.2 Biobase_2.29.1            
 [7] GenomicRanges_1.21.16      GenomeInfoDb_1.5.8        
 [9] IRanges_2.3.14             S4Vectors_0.7.10          
[11] BiocGenerics_0.15.3        BatchJobs_1.6             
[13] BiocParallel_1.3.34        BiocInstaller_1.19.8      

loaded via a namespace (and not attached):
 [1] magrittr_1.5         zlibbioc_1.15.0      brew_1.0-6          
 [4] sendmailR_1.2-1      stringr_1.0.0        tools_3.3.0         
 [7] fail_1.2             checkmate_1.6.0      DBI_0.3.1           
[10] lambda.r_1.1.7       futile.logger_1.4.1  digest_0.6.8        
[13] bitops_1.0-6         base64enc_0.1-2      futile.options_1.0.0
[16] RSQLite_1.0.0        stringi_0.5-5        BBmisc_1.9          

regards,
Arne

Note that Bioc-devel packages are only tested against R-release

http://bioconductor.org/checkResults/devel/bioc-LATEST/

This will be the case until the next release of bioc, at which point bioc devel will test against R-devel.

Hi - the error also occurs with R-3.2.0 and BiocDevel:

aln <- readGAlignments(bv)
Error in readGAlignments(bv) : 
  Assertion on 'more.args' failed: Vector must be named

Enter a frame number, or 0 to exit   

 1: readGAlignments(bv)
 2: readGAlignments(bv)
 3: Rsamtools:::.BamViews_delegate("readGAlignments", file, fun)
 4: bplapply(idx, fun, bamViews, ...)
 5: bplapply(idx, fun, bamViews, ...)
 6: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
 7: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = BPPARAM)
 8: suppressMessages(batchMap(reg, fun = FUN, X, more.args = list(...)))
 9: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessag
10: batchMap(reg, fun = FUN, X, more.args = list(...))
11: checkMoreArgs(more.args)
12: assertList(more.args, names = "strict")
13: makeAssertion(res, vname(x, .var.name))
14: mstop("Assertion on '%s' failed: %s", var.name, msg)

Seems there's a problem passing arguments from or to bplapply. Strange that this isn't picked up by the tests.

Arne

> sessionInfo()
R version 3.2.1 Patched (2015-07-06 r68635)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:

 [1] GenomicAlignments_1.5.11   Rsamtools_1.21.13         
 [3] Biostrings_2.37.2          XVector_0.9.1             
 [5] SummarizedExperiment_0.3.2 Biobase_2.29.1            
 [7] GenomicRanges_1.21.16      GenomeInfoDb_1.5.8        
 [9] IRanges_2.3.14             S4Vectors_0.7.10          
[11] BiocGenerics_0.15.3        BatchJobs_1.6             
[13] BiocParallel_1.3.34        BiocInstaller_1.19.8      

loaded via a namespace (and not attached):
 [1] magrittr_1.5         zlibbioc_1.15.0      brew_1.0-6          
 [4] sendmailR_1.2-1      stringr_1.0.0        tools_3.2.1         
 [7] fail_1.2             checkmate_1.6.0      DBI_0.3.1           
[10] lambda.r_1.1.7       futile.logger_1.4.1  digest_0.6.8        
[13] bitops_1.0-6         base64enc_0.1-2      futile.options_1.0.0
[16] RSQLite_1.0.0        stringi_0.5-5        BBmisc_1.9          

Hi Arne,

I can't reproduce this error in release or devel.

As Vince mentioned, this cycle we're using R 3.2.1 in both release and devel. You can see the R info at the top of the build reports, currently 3.2.1 (2015-06-18) -- "World-Famous Astronaut" in both.

http://www.bioconductor.org/checkResults/devel/bioc-LATEST/

http://www.bioconductor.org/checkResults/release/bioc-LATEST/

To checkout the patched version ...

svn co https://svn.r-project.org/R/branches/R-3-2-branch/

Valerie

Thanks, this was a bug in Rsamtools dispatch to BatchJobs back-end. It was introduced earlier in the 1.21.* series, and is fixed in version 1.21.14. For the record, the problem was reproducible with

library(GenomicAlignments)
library(BiocParallel)
register(BatchJobsParam())
fls <- system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE)
bv <- BamViews(fls, bamSamples=DataFrame(info="test", row.names="ex1"),
               auto.range=TRUE)
aln <- readGAlignments(bv)

Hi - thanks for this fix in Rsamtools, but this only fixes the problem in one place, there's another (and possibly more) in GenomicAlignments::summarizeOverlaps:

  mapq_filter <- function(features, reads, algorithm,
                             ignore.strand, inter.feature)
     { 
         require(GenomicAlignments) # needed for parallel evaluation
         Union(features, reads[mcols(reads)$mapq >= 20], algorithm,
               ignore.strand, inter.feature) 
     }

     genes <- GRanges("seq1", IRanges(seq(1, 1500, by=200), width=100))
     param <- ScanBamParam(what="mapq")
     fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
     se <- summarizeOverlaps(genes, fl, mode=mapq_filter, param=param) 

Error in summarizeOverlaps(genes, fl, mode = mapq_filter, param = param) : 
  Assertion on 'more.args' failed: Vector must be named

To me it looks like bplapply has changed it's interface and all the consumers of it that do not use names arguments now fail.

regards,

  Arne