Hi, I've recently installed R2.11.0 and BioC2.6 (MacBook Pro). While in the i386-apple-darwin9.8.0 the package "ShortRead" works fine, when I tried the same in the x86_64-apple-darwin9.8.0 the function "report" crashed with the following error: *** caught segfault *** address 0x110c0a110000, cause 'memory not mapped' Any clue? TIA, Hugo ##### CHUNK OF CODE #### library(ShortRead) exptPath <- system.file("extdata", package = "ShortRead") sp <- SolexaPath(exptPath) qaSummary <- qa(sp) report(qaSummary, dest = "/Users/kangu/tmp/qareport") #### MY SESSION #### [R.app GUI 1.33 (5582) x86_64-apple-darwin9.8.0] > library(ShortRead) Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from 'package:base': cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, table Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: lattice Loading required package: Rsamtools > exptPath <- system.file("extdata", package = "ShortRead") > sp <- SolexaPath(exptPath) > qaSummary <- qa(sp) > > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-apple-darwin9.8.0 locale: [1] es_ES.UTF-8/es_ES.UTF-8/C/C/es_ES.UTF-8/es_ES.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5 Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0 loaded via a namespace (and not attached): [1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 > > report(qaSummary, dest = "/Users/kangu/tmp/qareport") *** caught segfault *** address 0x110c0a110000, cause 'memory not mapped' Traceback: 1: .Call(fnname, ..., PACKAGE = "grid") 2: grid.Call("L_textBounds", as.graphicsAnnot(x$label), x$x, x $y, resolveHJust(x$just, x$hjust), resolveVJust(x$just, x $vjust), x$rot, 0) 3: widthDetails.text(x) 4: widthDetails(x) 5: function (x) { widthDetails(x)}(list(label = "", x = 0.5, y = 0.5, just = "centre", hjust = NULL, vjust = NULL, rot = 0, check.overlap = FALSE, name = "GRID.text.6", gp = list(), vp = NULL)) 6: .Call.graphics(fnname, ..., PACKAGE = "grid") 7: grid.Call.graphics("L_setviewport", pvp, TRUE) 8: push.vp.viewport(X[[1L]], ...) 9: FUN(X[[1L]], ...) 10: lapply(vps, push.vp, recording) 11: pushViewport(viewport(layout = page.layout, gp = global.gpar, name = trellis.vpname("toplevel", prefix = prefix))) 12: printFunction(x, ...) 13: print.trellis(fig) 14: print(fig) 15: .html_img(dir, file, .plotReadQuality(df[df$type == type, ]), ...) 16: .htmlReadQuality(dest, "readQuality", qa) 17: func(x, dest, type, ...) 18: func(x, dest, type, ...) 19: report(qaSummary, dest = "/Users/kangu/tmp/qareport") 20: report(qaSummary, dest = "/Users/kangu/tmp/qareport") 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:

Hi, the issue was solved in ShortRead_1.6.2. Thank you, Hugo El 28/04/2010, a las 03:38 p.m., Hugo Naya escribi?: > Hi, > I've recently installed R2.11.0 and BioC2.6 (MacBook Pro). While in > the i386-apple-darwin9.8.0 the package "ShortRead" works fine, when > I tried the same in the x86_64-apple-darwin9.8.0 the function > "report" crashed with the following error: > > *** caught segfault *** > address 0x110c0a110000, cause 'memory not mapped' > > Any clue? > TIA, > > Hugo > > > ##### CHUNK OF CODE #### > library(ShortRead) > exptPath <- system.file("extdata", package = "ShortRead") > sp <- SolexaPath(exptPath) > qaSummary <- qa(sp) > report(qaSummary, dest = "/Users/kangu/tmp/qareport") > > > > > #### MY SESSION #### > > [R.app GUI 1.33 (5582) x86_64-apple-darwin9.8.0] > > > library(ShortRead) > Loading required package: IRanges > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:base': > > cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, > rbind, rep.int, table > > Loading required package: GenomicRanges > Loading required package: Biostrings > Loading required package: lattice > Loading required package: Rsamtools > > exptPath <- system.file("extdata", package = "ShortRead") > > sp <- SolexaPath(exptPath) > > qaSummary <- qa(sp) > > > > sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-apple-darwin9.8.0 > > locale: > [1] es_ES.UTF-8/es_ES.UTF-8/C/C/es_ES.UTF-8/es_ES.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5 > Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2 > > > > report(qaSummary, dest = "/Users/kangu/tmp/qareport") > > *** caught segfault *** > address 0x110c0a110000, cause 'memory not mapped' > > Traceback: > 1: .Call(fnname, ..., PACKAGE = "grid") > 2: grid.Call("L_textBounds", as.graphicsAnnot(x$label), x$x, x > $y, resolveHJust(x$just, x$hjust), resolveVJust(x$just, x > $vjust), x$rot, 0) > 3: widthDetails.text(x) > 4: widthDetails(x) > 5: function (x) { widthDetails(x)}(list(label = "", x = 0.5, y = > 0.5, just = "centre", hjust = NULL, vjust = NULL, rot = 0, > check.overlap = FALSE, name = "GRID.text.6", gp = list(), vp = > NULL)) > 6: .Call.graphics(fnname, ..., PACKAGE = "grid") > 7: grid.Call.graphics("L_setviewport", pvp, TRUE) > 8: push.vp.viewport(X[[1L]], ...) > 9: FUN(X[[1L]], ...) > 10: lapply(vps, push.vp, recording) > 11: pushViewport(viewport(layout = page.layout, gp = > global.gpar, name = trellis.vpname("toplevel", prefix = prefix))) > 12: printFunction(x, ...) > 13: print.trellis(fig) > 14: print(fig) > 15: .html_img(dir, file, .plotReadQuality(df[df$type == > type, ]), ...) > 16: .htmlReadQuality(dest, "readQuality", qa) > 17: func(x, dest, type, ...) > 18: func(x, dest, type, ...) > 19: report(qaSummary, dest = "/Users/kangu/tmp/qareport") > 20: report(qaSummary, dest = "/Users/kangu/tmp/qareport") > > 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: > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor