The same command was working before.

my_SV<- makeGenomicInteractionsFromFile("my-sv.bedpe" , 
                                type="bedpe", 
                                experiment_name="my experiment", 
                                description="structural variants")

my_SV

GenomicInteractions object with 12933 interactions and 0 metadata columns:
    Name: my experiment
    Description: structural variants
    Sum of interactions: 611509
    Annotated:  no 
    Interactions:
Error in `rownames<-`(`*tmp*`, value = c("    [1]", "    [2]", "    [3]",  : 
  length of 'dimnames' [1] not equal to array extent


> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.1 (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] ggplot2_2.0.0             tidyr_0.3.1               dplyr_0.4.3               GenomicInteractions_1.4.1
[5] GenomicRanges_1.22.4      GenomeInfoDb_1.6.3        IRanges_2.4.6             S4Vectors_0.8.11         
[9] BiocGenerics_0.16.1      

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.0.2 VariantAnnotation_1.16.4   splines_3.2.3              lattice_0.20-33           
 [5] colorspace_1.2-6           rtracklayer_1.30.1         GenomicFeatures_1.22.7     chron_2.3-47              
 [9] survival_2.38-3            XML_3.98-1.3               foreign_0.8-66             DBI_0.3.1                 
[13] BiocParallel_1.4.3         RColorBrewer_1.1-2         lambda.r_1.1.7             matrixStats_0.50.1        
[17] plyr_1.8.3                 stringr_1.0.0              zlibbioc_1.16.0            Biostrings_2.38.3         
[21] munsell_0.4.2              gtable_0.1.2               futile.logger_1.4.1        latticeExtra_0.6-26       
[25] Biobase_2.30.0             biomaRt_2.26.1             AnnotationDbi_1.32.3       Rcpp_0.12.3               
[29] acepack_1.3-3.3            scales_0.3.0               BSgenome_1.38.0            Hmisc_3.17-1              
[33] Gviz_1.14.2                XVector_0.10.0             Rsamtools_1.22.0           gridExtra_2.0.0           
[37] digest_0.6.9               stringi_1.0-1              biovizBase_1.18.0          grid_3.2.3                
[41] tools_3.2.3                bitops_1.0-6               magrittr_1.5               RCurl_1.95-4.7            
[45] RSQLite_1.0.0              dichromat_2.0-0            Formula_1.2-1              cluster_2.0.3             
[49] futile.options_1.0.0       data.table_1.9.6           assertthat_0.1             R6_2.1.1                  
[53] rpart_4.1-10               GenomicAlignments_1.6.3    nnet_7.3-11                igraph_1.0.1              

Hi,

I think this should be fixed in the most recent version of GenomicInteractions in release, which is 1.4.2. If you have problems after updating to that version, let me know. This was due to changes in S4Vectors.

Thanks,

Liz