illegal operand when I run DEXSeq
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Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 18 hours ago
United States
Hi All, I got illegal operation when I run DEXSeq. May I know the possible reasons for this error? Follows are outputs of log file: R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > load('DEXseq.RData') > library(DEXSeq) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ?BiocGenerics? The following object(s) are masked from ?package:stats?: xtabs The following object(s) are masked from ?package:base?: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > ecs <- estimateDispersions(ecs) *** caught illegal operation *** address 0x2b101e337220, cause 'illegal operand' Traceback: 1: drop(exp(X %*% beta + offset)) 2: glmnb.fit(mm, y, initialGuess, mf$offset, coef.start = start) 3: fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, coef.start = start)) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 8: try(fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, coef.start = start)), silent = TRUE) 9: FUN(c("ENSMUSG00000073295", "ENSMUSG00000073293", "ENSMUSG00000068270", "ENSMUSG00000062393", "ENSMUSG00000004317", "ENSMUSG00000046269", "ENSMUSG00000087252", "ENSMUSG00000063018", "ENSMUSG00000039556", "ENSMUSG00000039545", "ENSMUSG00000039521", "ENSMUSG00000031143", "ENSMUSG00000031142", "ENSMUSG00000031144", "ENSMUSG00000031145", "ENSMUSG00000031146", "ENSMUSG00000031147", "ENSMUSG00000031148", "ENSMUSG00000039382", "ENSMUSG00000031149", "ENSMUSG00000031150", "ENSMUSG00000000134", "ENSMUSG00000031153", "ENSMUSG00000009731", 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"ENSMUSG00000027575", "ENSMUSG00000016356", "ENSMUSG00000027577", "ENSMUSG00000016349", "ENSMUSG00000016344", "ENSMUSG00000047841", "ENSMUSG00000027580", "ENSMUSG00000038705", "ENSMUSG00000084033", "ENSMUSG00000038671", "ENSMUSG00000027582", "ENSMUSG00000090077", "ENSMUSG00000085028", "ENSMUSG00000027583", "ENSMUSG00000000827", "ENSMUSG00000000826", "ENSMUSG00000089917", "ENSMUSG00000010492", "ENSMUSG00000000823", "ENSMUSG00000002455", "ENSMUSG00000038605", "ENSMUSG00000059540", "ENSMUSG00000002458", "ENSMUSG00000027584", "ENSMUSG00000027589", "ENSMUSG00000038628", "ENSMUSG00000096438", "ENSMUSG00000095134", "ENSMUSG00000096768")[[1L]], ...) 10: lapply(testablegenes, function(gn) { y <- modelFrames[[gn]]$count y1 <- pmax(y, 1/6) mf <- modelFrames[[gn]] mm <- modelmatrices[[gn]] fit <- lm.fit(mm, log(y1) - mf$offset) mm <- mm[, !is.na(fit$coefficients)] if (nrow(mm) <= ncol(mm)) stop("Underdetermined model; cannot estimate dispersions. Maybe replicates have not been properly specified.") start <- fit$coefficients[!is.na(fit$coefficients)] muhat <- try(fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, coef.start = start)), silent = TRUE) muhat}) 11: .local(object, ...) 12: estimateDispersions(ecs) 13: estimateDispersions(ecs) aborting ... Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu
DEXSeq DEXSeq • 1.7k views
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@steve-lianoglou-2771
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Hi, On Wed, Feb 27, 2013 at 4:04 PM, Ou, Jianhong <jianhong.ou at="" umassmed.edu=""> wrote: > Hi All, > > I got illegal operation when I run DEXSeq. > > May I know the possible reasons for this error? Can you show the output of `sessionInfo()` after you load DEXSeq so we can see the package versions you are using? (also, please be more prudent in the size of the "log" you paste into the email you send to the list ... having a list of all of the genes in your study is a bit much ;-) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Hi Steve, Because R is crashed after I run the code, I can only show you my sessionInfo before that. > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-unknown-linux-gnu (64-bit) 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=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0 [4] BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] biomaRt_2.14.0 hwriter_1.3 RCurl_1.95-3 statmod_1.4.16 stringr_0.6.2 [6] tools_2.15.2 XML_3.95-0.1 Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Feb 27, 2013, at 4:32 PM, Steve Lianoglou wrote: > Hi, > > On Wed, Feb 27, 2013 at 4:04 PM, Ou, Jianhong <jianhong.ou at="" umassmed.edu=""> wrote: >> Hi All, >> >> I got illegal operation when I run DEXSeq. >> >> May I know the possible reasons for this error? > > Can you show the output of `sessionInfo()` after you load DEXSeq so we > can see the package versions you are using? > > (also, please be more prudent in the size of the "log" you paste into > the email you send to the list ... having a list of all of the genes > in your study is a bit much ;-) > > -steve > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact
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Hi, I just wanted to ensure that you were using the latest version of the DEXSeq package, which you are. I'm not sure what other help I can offer other than the suggestion that it seems like it's time to do a bit more in depth debugging on your part, which won't be too easy if you're not comfortable with doing these types of things. >From your original output, it seems like the problem must be somewhere in the top 100 genes being tested, since there wasn't a "." printed to the console (I think it prints that every ~ 100 genes to keep you informed of it's progress). Perhaps you can see if it works when you exclude the top 100 genes, and debug backwards from there? Digging into the estimateDispersions function and having it print to the console the name of each gene as it is estimating dispersions would be another idea. All of this is assuming that your input data is sane, which we have no way to verify from our end. Are the `counts()` of your ExonCountSet sane, for starters? -steve On Wed, Feb 27, 2013 at 4:40 PM, Ou, Jianhong <jianhong.ou at="" umassmed.edu=""> wrote: > Hi Steve, > > Because R is crashed after I run the code, I can only show you my sessionInfo before that. > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0 > [4] BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] biomaRt_2.14.0 hwriter_1.3 RCurl_1.95-3 statmod_1.4.16 stringr_0.6.2 > [6] tools_2.15.2 XML_3.95-0.1 > > > Yours sincerely, > > Jianhong Ou > > jianhong.ou at umassmed.edu > > > On Feb 27, 2013, at 4:32 PM, Steve Lianoglou wrote: > >> Hi, >> >> On Wed, Feb 27, 2013 at 4:04 PM, Ou, Jianhong <jianhong.ou at="" umassmed.edu=""> wrote: >>> Hi All, >>> >>> I got illegal operation when I run DEXSeq. >>> >>> May I know the possible reasons for this error? >> >> Can you show the output of `sessionInfo()` after you load DEXSeq so we >> can see the package versions you are using? >> >> (also, please be more prudent in the size of the "log" you paste into >> the email you send to the list ... having a list of all of the genes >> in your study is a bit much ;-) >> >> -steve >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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On 2/27/2013 4:48 PM, Steve Lianoglou wrote: > Hi, > > I just wanted to ensure that you were using the latest version of the > DEXSeq package, which you are. > > I'm not sure what other help I can offer other than the suggestion > that it seems like it's time to do a bit more in depth debugging on > your part, which won't be too easy if you're not comfortable with > doing these types of things. > This > ecs <- estimateDispersions(ecs) *** caught illegal operation *** address 0x2b101e337220, cause 'illegal operand' is a bug at the C level. Here... Traceback: 1: drop(exp(X %*% beta + offset)) 2: glmnb.fit(mm, y, initialGuess, mf$offset, coef.start = start) 3: fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, coef.start = start)) ... suggests that things are going wrong in drop(), but it could be that the error occurs before this. I looked at the C code in drop() for likely candidates, but did not have success. You might gain some hints with trace(drop, quote(print(str(x)))) ecs <- estimateDispersions(ecs) which will print out an abbreviated version of the argument that drop() sees; perhaps it is unusual in some way? On linux you can try debugging C code, as in http://bioconductor.org/developers/c-debugging/ The 'valgrind' section is probably less intimidating that gdb. it might be easier to create as minimal a subset of 'ecs' as possible that still reproduces the example, and share that either with the list or more narrowly. Hope that helps, Martin >>From your original output, it seems like the problem must be somewhere > in the top 100 genes being tested, since there wasn't a "." printed to > the console (I think it prints that every ~ 100 genes to keep you > informed of it's progress). > > Perhaps you can see if it works when you exclude the top 100 genes, > and debug backwards from there? > > Digging into the estimateDispersions function and having it print to > the console the name of each gene as it is estimating dispersions > would be another idea. > > All of this is assuming that your input data is sane, which we have no > way to verify from our end. Are the `counts()` of your ExonCountSet > sane, for starters? > > -steve > > On Wed, Feb 27, 2013 at 4:40 PM, Ou, Jianhong <jianhong.ou at="" umassmed.edu=""> wrote: >> Hi Steve, >> >> Because R is crashed after I run the code, I can only show you my sessionInfo before that. >> >>> sessionInfo() >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> 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=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] DEXSeq_1.4.0 Biobase_2.18.0 BiocGenerics_0.4.0 >> [4] BiocInstaller_1.8.3 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.14.0 hwriter_1.3 RCurl_1.95-3 statmod_1.4.16 stringr_0.6.2 >> [6] tools_2.15.2 XML_3.95-0.1 >> >> >> Yours sincerely, >> >> Jianhong Ou >> >> jianhong.ou at umassmed.edu >> >> >> On Feb 27, 2013, at 4:32 PM, Steve Lianoglou wrote: >> >>> Hi, >>> >>> On Wed, Feb 27, 2013 at 4:04 PM, Ou, Jianhong <jianhong.ou at="" umassmed.edu=""> wrote: >>>> Hi All, >>>> >>>> I got illegal operation when I run DEXSeq. >>>> >>>> May I know the possible reasons for this error? >>> >>> Can you show the output of `sessionInfo()` after you load DEXSeq so we >>> can see the package versions you are using? >>> >>> (also, please be more prudent in the size of the "log" you paste into >>> the email you send to the list ... having a list of all of the genes >>> in your study is a bit much ;-) >>> >>> -steve >>> -- >>> Steve Lianoglou >>> Graduate Student: Computational Systems Biology >>> | Memorial Sloan-Kettering Cancer Center >>> | Weill Medical College of Cornell University >>> Contact Info: http://cbio.mskcc.org/~lianos/contact >> > > > -- Dr. Martin Morgan, PhD Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
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