BSgenome coercion to GRanges fails in singularity container

[omsai]

Trying to coerce a BSgenome object to GRanges gives no return value in the container created by coregenomics/singularity-kmap

> library(kmap)
> bsgenome <- BSgenome::getBSgenome("hg38")
> as(bsgenome, "GRanges")
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
[1] C

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.1 BSgenome_1.44.1                  
 [3] rtracklayer_1.36.4                Biostrings_2.44.2                
 [5] XVector_0.16.0                    GenomicRanges_1.28.4             
 [7] GenomeInfoDb_1.12.2               IRanges_2.10.3                   
 [9] S4Vectors_0.14.3                  BiocGenerics_0.22.0              
[11] kmap_0.1.0                       

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.6.3 QuasR_1.16.0              
 [3] VariantAnnotation_1.22.3   lattice_0.20-35           
 [5] BiocFileCache_1.0.1        GenomicFeatures_1.28.4    
 [7] blob_1.1.0                 XML_3.98-1.9              
 [9] rlang_0.1.2                glue_1.1.1                
[11] DBI_0.7                    BiocParallel_1.10.1       
[13] rappdirs_0.3.1             bit64_0.9-7               
[15] dbplyr_1.1.0               RColorBrewer_1.1-2        
[17] bindrcpp_0.2               plyr_1.8.4                
[19] matrixStats_0.52.2         GenomeInfoDbData_0.99.0   
[21] bindr_0.1                  zlibbioc_1.22.0           
[23] hwriter_1.3.2              memoise_1.1.0             
[25] latticeExtra_0.6-28        Biobase_2.36.2            
[27] biomaRt_2.32.1             BiocInstaller_1.26.1      
[29] AnnotationDbi_1.38.2       Rcpp_0.12.12              
[31] DelayedArray_0.2.7         ShortRead_1.34.1          
[33] bit_1.1-12                 Rsamtools_1.28.0          
[35] digest_0.6.12              dplyr_0.7.2               
[37] GenomicFiles_1.12.0        grid_3.4.1                
[39] tools_3.4.1                bitops_1.0-6              
[41] magrittr_1.5               RCurl_1.95-4.8            
[43] tibble_1.3.4               RSQLite_2.0               
[45] pkgconfig_2.0.1            Matrix_1.2-11             
[47] assertthat_0.2.0           httr_1.3.1                
[49] R6_2.2.2                   GenomicAlignments_1.12.2  
[51] Rbowtie_1.16.0             compiler_3.4.1  
>

[omsai]

It looks like there is generic method for coercion to GRanges that is getting preference:

> library(kmap)
> getMethod("coerce", signature = c(from="BSgenome", to="GRanges"))
Method Definition:

function (from, to = "GRanges", strict = TRUE) 
{
    gr <- GenomicRanges::makeGRangesFromDataFrame(data.frame(chr = seqnames(from), 
        start = rep(1, length(from)), end = seqlengths(from)), 
        ignore.strand = TRUE)
    names(gr) <- NULL
}
<environment: namespace:kmap>

Signatures:
        from       to       
target  "BSgenome" "GRanges"
defined "BSgenome" "GRanges"
> getMethod("coerce", signature = c(from="BSgenome", to="Views"))
Method Definition:

function (from, to = "Views", strict = TRUE) 
as(from, "BSgenomeViews")
<environment: namespace:kmap>

Signatures:
        from       to     
target  "BSgenome" "Views"
defined "BSgenome" "Views"
> getMethod("coerce", signature = c(from="BSgenome", to="BSgenomeViews"))
Method Definition:

function (from, to = "BSgenomeViews", strict = TRUE) 
BSgenomeViews(from, as(from, "GRanges"))
<environment: namespace:kmap>

Signatures:
        from       to             
target  "BSgenome" "BSgenomeViews"
defined "BSgenome" "BSgenomeViews"
>