I wrote an R function, setGt2Na(), taking a bgzipped VCF as input, setting genotypes to missing (i.e. GT to ".") when quality is below a threshold, and writing a new bgzipped VCF. Here is an example:

library(rutilstimflutre) # my personal R pkg, see below
setGt2Na(vcf.file="input.vcf.gz", genome="test", out.file="output.vcf", yieldSize=10000, min.gq=90)

But I receive the following error:

Error in unlist(Map(function(l, nm) { : error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in relist(from, PartitioningByEnd(seq_along(from), names = names(from))) : error in evaluating the argument 'skeleton' in selecting a method for function 'relist': Error: could not find function "PartitioningByEnd"

Following R debugging good practices, I do the following:

traceback()

which returns:

7: unlist(Map(function(l, nm) { ifelse(l, nm, NA_character_) }, info[logicals], as(names(info)[logicals], "List")))
6: .makeVcfInfo(info(obj), length(rd))
5: .makeVcfMatrix(filename, obj)
4: .local(obj, filename, ...)
3: VariantAnnotation::writeVcf(obj = vcf, filename = con)
2: VariantAnnotation::writeVcf(obj = vcf, filename = con)
1: setGt2Na(vcf.file = "input.vcf.gz", genome = "test", out.file = "output.vcf", yieldSize = 10000, min.gq = 90)

The PartitioningByEnd function belongs to thez IRanges package, which is in the Imports field of the DESCRIPTION file of the VariantAnnotation package. Moreover, my function does requireNamespace("IRanges") at the beginning.

So do you have any idea why this error is happening?

FYI the code of the setGt2Na() function is in my custom R pkg on GitHub. Note that, as this is my personal R pkg, it has many functions doing different stuff. To avoid having it to depend on too many packages from different fields (genomics, genetics, statistics, etc), I explicitly use requireNamespace("foo") when I need a function from the foo pkg in one of my function, as advised by Hadley Wickham in his book here.

Here is my sessionInfo():

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rutilstimflutre_0.15.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.32.0       XVector_0.10.0            
 [3] GenomicAlignments_1.6.0    GenomicRanges_1.22.0      
 [5] BiocGenerics_0.16.0        zlibbioc_1.16.0           
 [7] IRanges_2.4.0              BiocParallel_1.4.0        
 [9] BSgenome_1.38.0            GenomeInfoDb_1.6.0        
[11] tools_3.2.2                SummarizedExperiment_1.0.0
[13] parallel_3.2.2             Biobase_2.30.0            
[15] data.table_1.9.6           DBI_0.3.1                 
[17] lambda.r_1.1.7             futile.logger_1.4.1       
[19] rtracklayer_1.30.0         S4Vectors_0.8.0           
[21] futile.options_1.0.0       bitops_1.0-6              
[23] RCurl_1.95-4.7             biomaRt_2.26.0            
[25] RSQLite_1.0.0              compiler_3.2.2            
[27] GenomicFeatures_1.22.0     Rsamtools_1.22.0          
[29] Biostrings_2.38.0          XML_3.98-1.3              
[31] stats4_3.2.2               VariantAnnotation_1.16.0  
[33] chron_2.3-47              

It looks like Jim Hester fixed this in S4Vectors devel, but the change has not yet been ported to release.