Thanks Hervé! Best wishes
Leonard On Mon, Dec 7, 2015 at 12:08 AM, Hervé Pagès <[email protected]> wrote: > Hi Leonard, > > Thanks for the report. This segfault was due to a long-standing bug > in the "window" method for Rle objects when the object has length 0: > > > window(Rle(), 1, 0) # you might need to try many times before > # you get the segfault > *** caught segfault *** > address 0x12f69d74, cause 'memory not mapped' > > Traceback: > 1: .Call(.NAME, ..., PACKAGE = PACKAGE) > 2: .Call2("Rle_getStartEndRunAndOffset", x, start, end, PACKAGE = > "IRanges") > 3: getStartEndRunAndOffset(x, start(solved_SEW), end(solved_SEW)) > 4: .local(x, ...) > 5: window(Rle(), 1, 0) > 6: window(Rle(), 1, 0) > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: 2 > Save workspace image? [y/n/c]: > > It is now fixed in release (S4Vectors 0.8.4 and IRanges 2.4.5) and > devel (S4Vectors 0.9.12 and IRanges 2.5.10). > > Cheers, > H. > > > > On 12/05/2015 03:29 PM, Leonard Goldstein wrote: >> >> Hi all, >> >> I ran into problems when using an RleList as column in a DataFrame >> object (see example below). >> >> Many thanks in advance for your help. >> >> Leonard >> >> >>> sessionInfo() >> >> R version 3.2.2 (2015-08-14) >> Platform: x86_64-pc-linux-gnu (64-bit) >> Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] 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 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats4 parallel stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] IRanges_2.4.4 S4Vectors_0.8.3 BiocGenerics_0.16.1 >>> >>> >>> df <- DataFrame(ID = 1:3) >>> x <- RleList(IntegerList(vector("list", 3))) >>> df$rle <- x >>> df >> >> DataFrame with 3 rows and 2 columns >> >> *** caught segfault *** >> address 0x9b00364, cause 'memory not mapped' >> >> Traceback: >> 1: .Call(.NAME, ..., PACKAGE = PACKAGE) >> 2: .Call2("Rle_getStartEndRunAndOffset", x, start, end, PACKAGE = >> "S4Vectors") >> 3: S4Vectors:::getStartEndRunAndOffset(x, start(solved_SEW), >> end(solved_SEW)) >> 4: .local(x, ...) >> 5: window(x, start = 1L, width = n) >> 6: window(x, start = 1L, width = n) >> 7: .local(x, ...) >> 8: head(x, 3) >> 9: head(x, 3) >> >> Possible actions: >> 1: abort (with core dump, if enabled) >> 2: normal R exit >> 3: exit R without saving workspace >> 4: exit R saving workspace >> Selection: >> >> _______________________________________________ >> [email protected] mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: [email protected] > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
