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@queryHits
Using queryHits(fo) works, and using fo@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
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