[Bioc-devel] IRanges findOverlaps and queryHits

[Nathan Sheffield]

Did the findOverlaps return object get a @queryHits slot removed recently?

I recently got this error running some of my code:

Error: no slot of name "queryHits" for this object of class 
"SortedByQueryHits"

My workflow is basically,

fo = findOverlaps(...)
fo at queryHits

Using queryHits(fo) works, and using fo at queryHits to access it via slot 
has always worked for me as well -- until this time. I couldn't find 
anything in a changelog describing any changes into IRanges slots. 
Thought someone here might be able to shed some light on that for me... 
does anyone know what happened to the ability to access with @queryHits? 
Some relevant sessionInfo():

 > sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C 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 
LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C 
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] RGenomeUtils_0.01 BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99 
BSgenome.Hsapiens.UCSC.hg19_1.4.0
  [4] BSgenome_1.42.0 rtracklayer_1.34.1 Biostrings_2.42.0
  [7] XVector_0.14.0 LOLA_1.4.0 GenomicRanges_1.26.1
[10] GenomeInfoDb_1.10.1 IRanges_2.8.1 S4Vectors_0.12.0
[13] BiocGenerics_0.20.0 ggplot2_2.1.0 simpleCache_0.0.1
[16] extrafont_0.17 data.table_1.9.6 devtools_1.12.0
[19] project.init_0.0.1

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.7                plyr_1.8.4 bitops_1.0-6               
tools_3.3.0
  [5] zlibbioc_1.20.0            testthat_1.0.2 
digest_0.6.10              lattice_0.20-33
  [9] memoise_1.0.0              gtable_0.2.0 Matrix_1.2-6               
yaml_2.1.13
[13] Rttf2pt1_1.3.4             withr_1.0.2 stringr_1.1.0              
roxygen2_5.0.1
[17] grid_3.3.0                 Biobase_2.34.0 
R6_2.2.0                   BiocParallel_1.8.1
[21] XML_3.98-1.4               reshape2_1.4.2 
extrafontdb_1.0            magrittr_1.5
[25] GenomicAlignments_1.10.0   Rsamtools_1.26.1 
scales_0.4.1               SummarizedExperiment_1.4.0
[29] colorspace_1.3-0           stringi_1.1.2 RCurl_1.95-4.8             
munsell_0.4.3
[33] chron_2.3-47               crayon_1.3.2
 >


-Nathan