This message may be a bit premature or redundant since after writing it I now see that Herve is in the midst of work on the Hits class in S4Vectors.
My package GenomicTuples is currently failing R CMD check in the devel branch (http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicTuples/zin2-checksrc.html). I tracked down the error to a problem with my distanceToNearest,GTuples,GTuples-method. However, this is simply defined via inheritance to the distanceToNearest,GenomicRanges,GenomicRanges-method and so I believe the problem lies with the distanceToNearest,GenomicRanges,GenomicRanges-method. The following example adapted from nearest-methods {GenomicRanges} docs demonstrates the change in behaviour between the release and devel branch. It appears to be due to a new validity check of the Hits object returned by distanceToNearest. As I said, I now see that Herve recently started some work on the Hits class in S4Vectors, which includes this validity check, so this is really just a heads up that these changes affect the distanceToNearest method, in case this hasn't already been noted. Thanks, Pete #--------------------------------------------------------------------------------------------------- # BioC release > library(GenomicRanges) > query <- GRanges(c("A", "B"), IRanges(c(1, 5), width=1)) > subject <- GRanges("A", IRanges(c(6, 5, 13), c(10, 10, 15))) > distanceToNearest(query, subject) Hits of length 2 queryLength: 2 subjectLength: 3 queryHits subjectHits distance <integer> <integer> <integer> 1 1 2 3 2 2 NA NA > sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.18.1 GenomeInfoDb_1.2.2 IRanges_2.0.0 [4] S4Vectors_0.4.0 BiocGenerics_0.12.0 loaded via a namespace (and not attached): [1] XVector_0.6.0 #--------------------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------------------- # BioC devel > library(GenomicRanges) > query <- GRanges(c("A", "B"), IRanges(c(1, 5), width=1)) > subject <- GRanges("A", IRanges(c(6, 5, 13), c(10, 10, 15))) > distanceToNearest(query, subject) Error in validObject(.Object) : invalid class “Hits” object: 'subjectHits(x)' must contain non-NA values >= 1 and <= 'subjectLength(x)' > sessionInfo() R Under development (unstable) (2014-10-29 r66891) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.19.4 GenomeInfoDb_1.3.6 IRanges_2.1.5 [4] S4Vectors_0.5.3 BiocGenerics_0.13.0 loaded via a namespace (and not attached): [1] XVector_0.7.1 #--------------------------------------------------------------------------------------------------- -------------------------------- Peter Hickey, PhD Student/Research Assistant, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3052, Australia. Ph: +613 9345 2324 [email protected] http://www.wehi.edu.au ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}} _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
