[BioC] illegal operand when I run DEXSeq

Wolfgang Huber whuber at embl.de
Sun Mar 3 10:42:42 CET 2013


Dear Jianhong Ou

thanks for reporting. If you could make available a reproducible example (i.e. a minimal set of code and data files needed to reproduce your problem) we could try to figure out whether this is problem is specific to your R installation (e.g. how R and its packages were compiled) or a more generic problem in the software (as Martin says, the problem occurs in C code within the 'drop' function of R's 'base' package), and from there approach a solution.

	Best wishes
	Wolfgang

 
Il giorno Feb 27, 2013, alle ore 10:04 PM, "Ou, Jianhong" <Jianhong.Ou at umassmed.edu> ha scritto:

> 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)
> 
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> 
>> 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", "ENSMUSG00000031154", "ENSMUSG00000031155", "ENSMUSG00000031156", "ENSMUSG00000031157", "ENSMUSG00000031158", "ENSMUSG00000073291", "ENSMUSG00000039278", "ENSMUSG00000087193", "ENSMUSG00000039231", "ENSMUSG00000031165", "ENSMUSG00000086404", "ENSMUSG00000031166", "ENSMUSG00000031167", "ENSMUSG00000055188", "ENSMUSG00000039201", "ENSMUSG00000031168", "ENSMUSG00000031169", "ENSMUSG00000031171", "ENSMUSG00000079705", "ENSMUSG00000023165", "ENSMUSG00000079704", "ENSMUSG00000079702", "ENSMUSG00000079701", "ENSMUSG00000081410", "ENSMUSG00000079703", "ENSMUSG00000035371", "ENSMUSG00000071816", "ENSMUSG00000079699", "ENSMUSG00000079697", "ENSMUSG00000047344", "ENSMUSG00000079694", "ENSMUSG00000015342", "ENSMUSG00000015340", "ENSMUSG00000031176", "ENSMUSG00000054453", "ENSMUSG00000090084", "ENSMUSG00000031174", "ENSMUSG00000058254", "ENSMUSG00000008035", "ENSMUSG00000085587", "ENSMUSG00000040363", "ENSMUSG00000087271", "ENSMUSG00000031007", "ENSMUSG00000079871", "ENSMUSG00000044148", "ENSMUSG00000064127", "ENSMUSG00000085891", "ENSMUSG00000087424", "ENSMUSG00000084349", "ENSMUSG00000083364", "ENSMUSG00000000787", "ENSMUSG00000051228", "ENSMUSG00000031012", "ENSMUSG00000040229", "ENSMUSG00000047678", "ENSMUSG00000086048", "ENSMUSG00000025037", "ENSMUSG00000040147", "ENSMUSG00000040138", "ENSMUSG00000025040", "ENSMUSG00000037369", "ENSMUSG00000073274", "ENSMUSG00000037347", "ENSMUSG00000037341", "ENSMUSG00000087415", "ENSMUSG00000060090", 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"ENSMUSG00000027652", "ENSMUSG00000037761", "ENSMUSG00000027654", "ENSMUSG00000027655", "ENSMUSG00000070544", "ENSMUSG00000035877", "ENSMUSG00000085303", "ENSMUSG00000027412", "ENSMUSG00000053141", "ENSMUSG00000083567", "ENSMUSG00000016921", "ENSMUSG00000017858", "ENSMUSG00000017861", "ENSMUSG00000074607", "ENSMUSG00000017817", "ENSMUSG00000035399", "ENSMUSG00000017943", "ENSMUSG00000048486", "ENSMUSG00000017679", "ENSMUSG00000017707", "ENSMUSG00000035268", "ENSMUSG00000087129", "ENSMUSG00000017697", "ENSMUSG00000027656", "ENSMUSG00000018326", "ENSMUSG00000054582", "ENSMUSG00000018322", "ENSMUSG00000018209", "ENSMUSG00000017002", "ENSMUSG00000016995", "ENSMUSG00000017007", "ENSMUSG00000017009", "ENSMUSG00000045503", "ENSMUSG00000085760", "ENSMUSG00000090996", "ENSMUSG00000017720", "ENSMUSG00000017734", "ENSMUSG00000017721", "ENSMUSG00000017723", "ENSMUSG00000070533", "ENSMUSG00000070531", "ENSMUSG00000076434", "ENSMUSG00000039951", "ENSMUSG00000017299", "ENSMUSG00000086453", "ENSMUSG00000001403", "ENSMUSG00000017300", "ENSMUSG00000050373", "ENSMUSG00000017307", "ENSMUSG00000045822", "ENSMUSG00000017764", "ENSMUSG00000017767", "ENSMUSG00000039873", "ENSMUSG00000017760", "ENSMUSG00000017754", "ENSMUSG00000039849", "ENSMUSG00000039834", "ENSMUSG00000085436", "ENSMUSG00000017737", "ENSMUSG00000087503", "ENSMUSG00000017740", "ENSMUSG00000039804", "ENSMUSG00000017652", "ENSMUSG00000017664", "ENSMUSG00000017670", "ENSMUSG00000017667", "ENSMUSG00000027670", "ENSMUSG00000018459", "ENSMUSG00000039725", "ENSMUSG00000027661", "ENSMUSG00000017897", "ENSMUSG00000085274", "ENSMUSG00000086820", "ENSMUSG00000087351", "ENSMUSG00000027678", "ENSMUSG00000006800", "ENSMUSG00000039621", "ENSMUSG00000042854", "ENSMUSG00000074582", "ENSMUSG00000002718", "ENSMUSG00000090397", "ENSMUSG00000039536", "ENSMUSG00000082665", "ENSMUSG00000017999", "ENSMUSG00000039501", "ENSMUSG00000074578", "ENSMUSG00000086605", "ENSMUSG00000050556", "ENSMUSG00000085151", "ENSMUSG00000017969", "ENSMUSG00000017929", "ENSMUSG00000039463", "ENSMUSG00000047030", "ENSMUSG00000006418", "ENSMUSG00000042821", "ENSMUSG00000085596", "ENSMUSG00000078923", "ENSMUSG00000089739", "ENSMUSG00000090213", "ENSMUSG00000085914", "ENSMUSG00000006462", "ENSMUSG00000084797", "ENSMUSG00000087624", "ENSMUSG00000087684", "ENSMUSG00000027540", "ENSMUSG00000074577", "ENSMUSG00000044641", "ENSMUSG00000093752", "ENSMUSG00000051149", "ENSMUSG00000078919", "ENSMUSG00000074575", "ENSMUSG00000027544", "ENSMUSG00000027546", "ENSMUSG00000027551", "ENSMUSG00000052368", "ENSMUSG00000047907", "ENSMUSG00000096972", "ENSMUSG00000052056", "ENSMUSG00000052033", "ENSMUSG00000085495", "ENSMUSG00000027560", "ENSMUSG00000085949", "ENSMUSG00000027495", "ENSMUSG00000027496", "ENSMUSG00000027498", "ENSMUSG00000074570", "ENSMUSG00000027502", "ENSMUSG00000074569", "ENSMUSG00000027505", "ENSMUSG00000081344", "ENSMUSG00000028640", "ENSMUSG00000027509", "ENSMUSG00000027510", "ENSMUSG00000092596", "ENSMUSG00000087442", "ENSMUSG00000070495", "ENSMUSG00000027514", "ENSMUSG00000038400", "ENSMUSG00000087600", "ENSMUSG00000055897", "ENSMUSG00000027519", "ENSMUSG00000054455", "ENSMUSG00000027522", "ENSMUSG00000039263", "ENSMUSG00000086537", "ENSMUSG00000027523", "ENSMUSG00000090625", "ENSMUSG00000016253", "ENSMUSG00000016256", "ENSMUSG00000016252", "ENSMUSG00000016257", "ENSMUSG00000078906", "ENSMUSG00000078905", "ENSMUSG00000084050", "ENSMUSG00000080888", "ENSMUSG00000081949", "ENSMUSG00000090093", "ENSMUSG00000078902", "ENSMUSG00000078903", "ENSMUSG00000082376", "ENSMUSG00000084323", "ENSMUSG00000078901", "ENSMUSG00000078899", "ENSMUSG00000078898", "ENSMUSG00000078897", "ENSMUSG00000078896", "ENSMUSG00000094475", "ENSMUSG00000095545", "ENSMUSG00000094932", "ENSMUSG00000078889", "ENSMUSG00000083481", "ENSMUSG00000086941", "ENSMUSG00000078887", "ENSMUSG00000089756", "ENSMUSG00000078886", "ENSMUSG00000078891", "ENSMUSG00000085103", "ENSMUSG00000095648", "ENSMUSG00000086367", "ENSMUSG00000078894", "ENSMUSG00000094108", "ENSMUSG00000084858", "ENSMUSG00000078895", "ENSMUSG00000089951", "ENSMUSG00000078881", "ENSMUSG00000095199", "ENSMUSG00000078880", "ENSMUSG00000078879", "ENSMUSG00000078878", "ENSMUSG00000081599", "ENSMUSG00000078877", "ENSMUSG00000078876", "ENSMUSG00000083170", "ENSMUSG00000074527", "ENSMUSG00000094193", "ENSMUSG00000081326", "ENSMUSG00000078875", "ENSMUSG00000083317", "ENSMUSG00000083111", "ENSMUSG00000078872", "ENSMUSG00000082765", "ENSMUSG00000082724", "ENSMUSG00000081590", "ENSMUSG00000078870", "ENSMUSG00000083817", "ENSMUSG00000078869", "ENSMUSG00000078868", "ENSMUSG00000078867", "ENSMUSG00000082343", "ENSMUSG00000078866", "ENSMUSG00000094786", "ENSMUSG00000078865", "ENSMUSG00000080709", "ENSMUSG00000078864", "ENSMUSG00000095362", "ENSMUSG00000081574", "ENSMUSG00000074521", "ENSMUSG00000074529", "ENSMUSG00000078862", "ENSMUSG00000074519", "ENSMUSG00000097879", "ENSMUSG00000078861", "ENSMUSG00000027525", "ENSMUSG00000060445", "ENSMUSG00000070476", "ENSMUSG00000039155", "ENSMUSG00000000305", "ENSMUSG00000039117", "ENSMUSG00000085704", "ENSMUSG00000039108", "ENSMUSG00000027566", "ENSMUSG00000039086", "ENSMUSG00000039069", "ENSMUSG00000039050", "ENSMUSG00000039041", "ENSMUSG00000039001", "ENSMUSG00000038990", "ENSMUSG00000084843", "ENSMUSG00000038963", "ENSMUSG00000027568", "ENSMUSG00000027569", "ENSMUSG00000049401", "ENSMUSG00000027570", "ENSMUSG00000038932", "ENSMUSG00000038914", "ENSMUSG00000027573", "ENSMUSG00000023393", "ENSMUSG00000038848", "ENSMUSG00000027574", "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
> 
> _______________________________________________
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