d<-binOverGene(cvglist,tr,upstream.cutoff =1000,downstream.cutoff = 1000)

ERROR: subscript contains out-of-bounds ranges

Dear Wuze,

This is a bug in binOverGene when the accumulated given range for any chromosome is greater than 2^31. I tried to fix the bug in next release build (3.12.3). 

Let me know if you still have trouble in using next release build. 

Hi, could you please try with upstream.cutoff = 0, downstream.cutoff = 0? Also could you please provide your R session information by typing sessionInfo()? Thanks!

Best regards,

Julie

Yes, if i set upstream.cutoff = 0, downstream.cutoff = 0, it works, but i wanted to show some flanking  regions. 

and here was my sessioninfo:

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8       
 [4] LC_COLLATE=zh_CN.UTF-8     LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2   Biobase_2.36.2         GenomicRanges_1.28.6  
[5] GenomeInfoDb_1.12.3    IRanges_2.10.5         S4Vectors_0.14.7       BiocGenerics_0.22.1   

loaded via a namespace (and not attached):
 [1] httr_1.3.1                    bit64_0.9-7                   AnnotationHub_2.8.3          
 [4] splines_3.4.2                 shiny_1.0.5                   Formula_1.2-2                
 [7] interactiveDisplayBase_1.14.0 latticeExtra_0.6-28           RBGL_1.52.0                  
[10] blob_1.1.0                    BSgenome_1.44.2               GenomeInfoDbData_0.99.0      
[13] Rsamtools_1.28.0              yaml_2.1.14                   RSQLite_2.0                  
[16] backports_1.1.1               lattice_0.20-35               biovizBase_1.24.0            
[19] digest_0.6.12                 RColorBrewer_1.1-2            XVector_0.16.0               
[22] checkmate_1.8.5               colorspace_1.3-2              ggbio_1.24.1                 
[25] httpuv_1.3.5                  htmltools_0.3.6               Matrix_1.2-11                
[28] plyr_1.8.4                    OrganismDbi_1.18.1            XML_3.98-1.9                 
[31] pkgconfig_2.0.1               biomaRt_2.32.1                zlibbioc_1.22.0              
[34] xtable_1.8-2                  scales_0.5.0                  BiocParallel_1.10.1          
[37] htmlTable_1.9                 tibble_1.3.4                  AnnotationFilter_1.0.0       
[40] ggplot2_2.2.1                 SummarizedExperiment_1.6.5    nnet_7.3-12                  
[43] lazyeval_0.2.1                mime_0.5                      survival_2.41-3              
[46] magrittr_1.5                  memoise_1.1.0                 GGally_1.3.2                 
[49] foreign_0.8-69                graph_1.54.0                  BiocInstaller_1.26.1         
[52] tools_3.4.2                   data.table_1.10.4-3           matrixStats_0.52.2           
[55] stringr_1.2.0                 munsell_0.4.3                 cluster_2.0.6                
[58] DelayedArray_0.2.7            ensembldb_2.0.4               Biostrings_2.44.2            
[61] compiler_3.4.2                rlang_0.1.4                   grid_3.4.2                   
[64] RCurl_1.95-4.8                dichromat_2.0-0               VariantAnnotation_1.22.3     
[67] htmlwidgets_0.9               labeling_0.3                  bitops_1.0-6                 
[70] base64enc_0.1-3               gtable_0.2.0                  curl_3.0                     
[73] DBI_0.7                       reshape_0.8.7                 R6_2.2.2                     
[76] reshape2_1.4.2                GenomicAlignments_1.12.2      gridExtra_2.3                
[79] knitr_1.17                    rtracklayer_1.36.6            bit_1.1-12                   
[82] Hmisc_4.0-3                   ProtGenerics_1.8.0            stringi_1.1.6                
[85] Rcpp_0.12.13                  rpart_4.1-11                  acepack_1.4.1