Hi all

I have been getting the following error today on the files which worked fine yesterday : 

Error: subscript is a NSBS object that is incompatible with the current subsetting operation

Happened after I updated some bioconductor packages (don't remember which ones)

Reproducible example:

library("TxDb.Dmelanogaster.UCSC.dm6.ensGene")

seqlevelsStyle(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "ENSEMBL"

tss <- rtracklayer::import.bed(url("https://bit.ly/2J0rIbj"))

VariantAnnotation::locateVariants(
        query = tss,
        subject = TxDb.Dmelanogaster.UCSC.dm6.ensGene,
        VariantAnnotation::AllVariants(promoter = VariantAnnotation::PromoterVariants(
            upstream = 500, downstream = 0
            )) )

SessionInfo:

R version 3.5.0 (2018-04-23)

Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /package/R-3.5.0/lib64/R/lib/libRblas.so
LAPACK: /package/R-3.5.0/lib64/R/lib/libRlapack.so

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] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1
[2] GenomicFeatures_1.32.0                   
[3] AnnotationDbi_1.42.1                     
[4] Biobase_2.40.0                           
[5] GenomicRanges_1.32.3                     
[6] GenomeInfoDb_1.16.0                      
[7] IRanges_2.15.13                          
[8] S4Vectors_0.19.6                         
[9] BiocGenerics_0.26.0                      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17                compiler_3.5.0             
 [3] XVector_0.20.0              prettyunits_1.0.2          
 [5] bitops_1.0-6                tools_3.5.0                
 [7] progress_1.1.2              zlibbioc_1.26.0            
 [9] biomaRt_2.36.0              digest_0.6.15              
[11] bit_1.1-13                  BSgenome_1.48.0            
[13] lattice_0.20-35             RSQLite_2.1.1              
[15] memoise_1.1.0               pkgconfig_2.0.1            
[17] Matrix_1.2-14               DelayedArray_0.6.0         
[19] DBI_1.0.0                   GenomeInfoDbData_1.1.0     
[21] rtracklayer_1.40.2          stringr_1.3.1              
[23] httr_1.3.1                  Biostrings_2.48.0          
[25] grid_3.5.0                  bit64_0.9-7                
[27] R6_2.2.2                    XML_3.98-1.11              
[29] BiocParallel_1.15.5         blob_1.1.1                 
[31] magrittr_1.5                Rsamtools_1.32.0           
[33] matrixStats_0.53.1          GenomicAlignments_1.16.0   
[35] assertthat_0.2.0            SummarizedExperiment_1.10.1
[37] stringi_1.2.2               RCurl_1.95-4.10            
[39] VariantAnnotation_1.27.0

Any idea?

All right problem solved..!

The update of S4Vectors from 0.17 to 0.19 (from GitHub) caused VariantAnnotation functions to break. Downgrading (using biocLite) solved it.