I am struggling to reproduce, hoping developers would have an insight to this behaviour.

I am using rtracklayer::import() to subset bigWig data. Something like:

x <- import(files[i], which = gr)

After running above, as expected there is a GRanges x object and unexpected first_time object with a value of FALSE

Where is it coming from, any ideas?

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252 
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] rtracklayer_1.34.0   GenomicRanges_1.26.1 GenomeInfoDb_1.10.0  IRanges_2.8.0        S4Vectors_0.12.0  
[6] BiocGenerics_0.20.0  oncofunco_0.0.0.9000 ggrepel_0.6.3        ggplot2_2.1.0        dplyr_0.5.0       
[11] dtplyr_0.0.1         data.table_1.9.6    

loaded via a namespace (and not attached):
[1] Rcpp_0.12.7                XVector_0.14.0             magrittr_1.5               GenomicAlignments_1.10.0
[5] zlibbioc_1.20.0            BiocParallel_1.8.0         munsell_0.4.3              lattice_0.20-34         
[9] colorspace_1.2-7           R6_2.2.0                   plyr_1.8.4                 tools_3.3.1             
[13] SummarizedExperiment_1.4.0 grid_3.3.1                 Biobase_2.34.0             gtable_0.2.0            
[17] DBI_0.5-1                  assertthat_0.1             tibble_1.2                 Matrix_1.2-7.1          
[21] bitops_1.0-6               RCurl_1.95-4.8             labeling_0.3               seqminer_5.3            
[25] Rsamtools_1.26.1           Biostrings_2.42.0          scales_0.4.0               XML_3.98-1.4            
[29] chron_2.3-47 

I guess this is somehow coming from BiocGenerics:::unsafe_replaceSlots(). But I am not sure how, and obviously it doesn't reproduce on my end. Something like environment(unsafe_replaceSlots) <- .GlobalEnv would have had to happen somehow. Maybe you are using some sort of weird development mode in your IDE?