Hello, viewApply seems to not properly iterate over the views, but rather return the last view repeatedly. Minimal example : r <- Rle(1:1000) v <- Views(r, start=c(10, 100, 500), width = 1) > viewApply(v, function(x) x) [[1]] 'integer' Rle of length 1 with 1 run Lengths: 1 Values : 500 [[2]] 'integer' Rle of length 1 with 1 run Lengths: 1 Values : 500 [[3]] 'integer' Rle of length 1 with 1 run Lengths: 1 Values : 500 > sessionInfo() R version 2.12.0 (2010-10-15) 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=C 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] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.2.3 IRanges_1.8.8 loaded via a namespace (and not attached): [1] tools_2.12.0 -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia

On 02/10/2011 11:00 PM, Dario Strbenac wrote: > Hello, > > viewApply seems to not properly iterate over the views, but rather return the last view repeatedly. > > Minimal example : > > r <- Rle(1:1000) > v <- Views(r, start=c(10, 100, 500), width = 1) >> viewApply(v, function(x) x) > [[1]] > 'integer' Rle of length 1 with 1 run > Lengths: 1 > Values : 500 Thank you for the report; this bug, which would only be manifest when FUN returns the Rle in the view (not, e..g, viewApply(v, mean)), is fixed in IRanges v. 1.8.9 (release) / 1.9.22 (devel), which should be propagating to biocLite() in the next day or so. Martin > [[2]] > 'integer' Rle of length 1 with 1 run > Lengths: 1 > Values : 500 > > [[3]] > 'integer' Rle of length 1 with 1 run > Lengths: 1 > Values : 500 > >> sessionInfo() > R version 2.12.0 (2010-10-15) > 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=C 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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicRanges_1.2.3 IRanges_1.8.8 > > loaded via a namespace (and not attached): > [1] tools_2.12.0 > > -------------------------------------- > Dario Strbenac > Research Assistant > Cancer Epigenetics > Garvan Institute of Medical Research > Darlinghurst NSW 2010 > Australia > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793