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 <nat...@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@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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
