[Bioc-devel] IRanges findOverlaps and queryHits

[Michael Lawrence]

Hi Nathan,

Direct slot access is strongly discouraged, for this very reason. Please
stick to using the accessor.

And yes, Hits was redefined in terms of a graph model last devel cycle.

Michael

On Tue, Dec 20, 2016 at 12:16 PM, Nathan Sheffield <nathan at code.databio.org>
wrote:

> 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
>
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