Since after 10 min of googling I still cannot find the bug tracking system for bioconductor I am posting a bug report here. The problem is import function calls parseURI on file names:

   library(rtracklayer)
   import.bed("my bed file.bed")
Error in parseURI(uri) : cannot parse URI my bed file.bed
   traceback()
12: .Call("R_parseURI", as.character(uri), PACKAGE = "XML")
11: parseURI(uri)
10: .parseURI(resource)
9: connectionForResource(resource)
8: queryForConnection(con, which)
7: .local(con, format, text, ...)
6: import(FileForFormat(con, format), ...)
5: import(FileForFormat(con, format), ...)
4: import(con, format = "bed", ...)
3: import(con, format = "bed", ...)
2: import.bed("my bed file.bed")
1: import.bed("my bed file.bed")


sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] XML_3.98-1.3                       BSgenome.Drerio.UCSC.danRer7_1.4.0 BSgenome_1.36.3                   
 [4] Biostrings_2.36.2                  XVector_0.8.0                      gplots_2.17.0                     
 [7] rtracklayer_1.28.7                 GenomicRanges_1.20.5               GenomeInfoDb_1.4.1                
[10] IRanges_2.2.7                      S4Vectors_0.6.3                    BiocGenerics_0.14.0               
[13] genomation_1.1.10                  BiocParallel_1.2.20                colorout_1.1-0                    
[16] BiocInstaller_1.18.4              

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.0             futile.logger_1.4.1     plyr_1.8.3              bitops_1.0-6            futile.options_1.0.0   
 [6] tools_3.2.1             zlibbioc_1.14.0         digest_0.6.8            RSQLite_1.0.0           gtable_0.1.2           
[11] gridBase_0.4-7          DBI_0.3.1               proto_0.3-10            stringr_1.0.0           caTools_1.17.1         
[16] gtools_3.5.0            data.table_1.9.4        impute_1.42.0           plotrix_3.5-12          gdata_2.17.0           
[21] ggplot2_1.0.1           reshape2_1.4.1          readr_0.1.1             lambda.r_1.1.7          magrittr_1.5           
[26] matrixStats_0.14.2      Rsamtools_1.20.4        scales_0.2.5            GenomicAlignments_1.4.1 MASS_7.3-43            
[31] colorspace_1.2-6        KernSmooth_2.23-15      stringi_0.5-5           RCurl_1.95-4.7          munsell_0.4.2          
[36] chron_2.3-47          

I have fixed this, just testing now. Should be checked in release/devel sometime this morning.

Hi,

It looks like the spaces in the file name is the problem. The argument to parseURI()  must be a single string with no spaces (see ?parseURI). The error can be reproduced with

library(XML)

parseURI("my bed file.bed")

Valerie