Hello, I ran into a segfault while trying to run rqubic on a 2189x9779 matrix of integers (actually of mode 'numeric', named "data.exp.discr...") with values 0 through 6 (not a microarray dataset). I'm not sure if the error is in the way I made the rqubicSeeds and ExpressionSet objects from my matrix, or something internal to rqubic. The segfault is reproducible and occurs a few seconds after calling the function. The error message is copied below. Thanks, Eric Liaw undergraduate student, Stanford University ------------------------------------- > data.exprs <- new("ExpressionSet", data) #data is a matrix. > data.seeds <- generateSeeds(object=data.exprs) Warning message: In .local(object, ...) : 'generateSeeds' requires an matrix of integer. Coerced > QUBIC.1 <- quBicluster(seeds=data.seeds, eset=data.exprs, report.no=30) *** caught segfault *** address 0xffffffff1efabdd0, cause 'memory not mapped' Traceback: 1: .Call("qubicluster", seeds = seeds, exprs = exp.leveled, sigma_val = sigma, symbols = symbols, report_no = report.no, tolerance_val = tolerance, filter_proportion = filter.proportion) 2: quBiclusterIndex(seeds = seeds, eset = eset, report.no = report.no, tolerance = tolerance, filter.proportion = filter.proportion) 3: quBicluster(seeds = data.seeds, eset = data.exprs, report.no = 30) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace In quBiclusterIndex(seeds = seeds, eset = eset, report.no = report.no, : 'eset' requires an matrix of integer as the value of 'exprs'. Coerced -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rqubic_1.4.0 biclust_1.0.2 lattice_0.20-13 colorspace_1.0-1 [5] MASS_7.3-23 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] tools_2.15.2 -- Sent via the guest posting facility at bioconductor.org.

Dear Eric, Thanks for reporting the issue. I will look into it. Do you mind sending me the data that you used so that I could reproduce the errors? Best wishes, David On Sun, May 11, 2014 at 9:13 AM, Eric Liaw [guest] <guest@bioconductor.org>wrote: > Hello, > > I ran into a segfault while trying to run rqubic on a 2189x9779 matrix of > integers (actually of mode 'numeric', named "data.exp.discr...") with > values 0 through 6 (not a microarray dataset). I'm not sure if the error is > in the way I made the rqubicSeeds and ExpressionSet objects from my matrix, > or something internal to rqubic. The segfault is reproducible and occurs a > few seconds after calling the function. > > The error message is copied below. > > Thanks, > Eric Liaw > undergraduate student, Stanford University > ------------------------------------- > > > data.exprs <- new("ExpressionSet", data) #data is a matrix. > > data.seeds <- generateSeeds(object=data.exprs) > > Warning message: > In .local(object, ...) : > 'generateSeeds' requires an matrix of integer. Coerced > > > QUBIC.1 <- quBicluster(seeds=data.seeds, eset=data.exprs, report.no=30) > > *** caught segfault *** > address 0xffffffff1efabdd0, cause 'memory not mapped' > > Traceback: > 1: .Call("qubicluster", seeds = seeds, exprs = exp.leveled, sigma_val = > sigma, symbols = symbols, report_no = report.no, tolerance_val = > tolerance, filter_proportion = filter.proportion) > 2: quBiclusterIndex(seeds = seeds, eset = eset, report.no = report.no, > tolerance = tolerance, filter.proportion = filter.proportion) > 3: quBicluster(seeds = data.seeds, eset = data.exprs, report.no = 30) > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > > In quBiclusterIndex(seeds = seeds, eset = eset, report.no = report.no, : > 'eset' requires an matrix of integer as the value of 'exprs'. Coerced > > -- output of sessionInfo(): > > R version 2.15.2 (2012-10-26) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] rqubic_1.4.0 biclust_1.0.2 lattice_0.20-13 > colorspace_1.0-1 > [5] MASS_7.3-23 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] tools_2.15.2 > > > -- > Sent via the guest posting facility at bioconductor.org. > -- *Dr. Jitao David Zhang | **张继涛** | Computational Biology and Bioinformatics | Pharmaceutical Divison | F. Hoffmann-La-Roche AG | CH-4070 Basel | Switzerland* *Tel +41 61 688 62 51 * Confidentiality Note: This message is intended only for ...{{dropped:11}}