Question: load methylKit segfault error
0
gravatar for tangming2005
3.2 years ago by
tangming2005150
United States
tangming2005150 wrote:

I installed methylKit, but when I load it, I had segfault error below. I had similar problem with dplyr, and I have to 

re-install R and it was OK. not sure it is the same problem.  

Thanks very much!

Ming

 

I can not run sessionInfo after load the library, before I load methylKit:

 sessionInfo()

R version 3.3.1 (2016-06-21)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X 10.11.5 (El Capitan)


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base 


 library(methylKit)

Loading required package: GenomicRanges

Loading required package: BiocGenerics

Loading required package: parallel


Attaching package: ‘BiocGenerics’


The following objects are masked from ‘package:parallel’:


    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,

    clusterExport, clusterMap, parApply, parCapply, parLapply,

    parLapplyLB, parRapply, parSapply, parSapplyLB


The following objects are masked from ‘package:stats’:


    IQR, mad, xtabs


The following objects are masked from ‘package:base’:


    anyDuplicated, append, as.data.frame, cbind, colnames, do.call,

    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,

    is.unsorted, lapply, lengths, Map, mapply, match, mget, order,

    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,

    Reduce, rownames, sapply, setdiff, sort, table, tapply, union,

    unique, unsplit


Loading required package: S4Vectors

Loading required package: stats4


Attaching package: ‘S4Vectors’


The following objects are masked from ‘package:base’:


    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: IRanges

Loading required package: GenomeInfoDb


 *** caught segfault ***

address 0x18, cause 'memory not mapped'


Traceback:

 1: dyn.load(file, DLLpath = DLLpath, ...)

 2: library.dynam(lib, package, package.lib)

 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])

 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)

 5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])

 6: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)

 7: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])

 8: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)

 9: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])

10: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)

11: loadNamespace(package, lib.loc)

12: doTryCatch(return(expr), name, parentenv, handler)

13: tryCatchOne(expr, names, parentenv, handlers[[1L]])

14: tryCatchList(expr, classes, parentenv, handlers)

15: 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))})

16: try({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)})

17: library(methylKit)


Possible actions:

1: abort (with core dump, if enabled)

2: normal R exit

3: exit R without saving workspace

4: exit R saving workspace
bioconductor methylkit • 727 views
ADD COMMENTlink modified 3.2 years ago by Martin Morgan ♦♦ 24k • written 3.2 years ago by tangming2005150
Answer: load methylKit segfault error
0
gravatar for altuna akalin
3.2 years ago by
Germany/Berlin/MDC-BIMSB
altuna akalin20 wrote:

I'm not sure if this will help but can you try to install it from github. Currently, package passes tests so it can be loaded and used on the test environments and our own machines.

library(devtools)
install_github("al2na/methylKit", build_vignettes=FALSE,
    repos=BiocInstaller::biocinstallRepos(), dependencies=TRUE)
ADD COMMENTlink modified 3.2 years ago by Martin Morgan ♦♦ 24k • written 3.2 years ago by altuna akalin20

biocLite("al2na/methylKit", dependencies=TRUE) is another version of this (it calls devtools::install_github() 'under the hood'); it seems moderately preferable because one cannot 'forget' the repos argument and hence less likely to get a mixture of Bioconductor package versions.

ADD REPLYlink written 3.2 years ago by Martin Morgan ♦♦ 24k

I reinstalled R and then install below and it seems to be working now. Thanks!

source("http://bioconductor.org/biocLite.R")
biocLite(c('IRanges', 'data.table', 'S4Vectors', 'GenomeInfoDb', 'KernSmooth', 
                 'qvalue', 'emdbook', 'Rsamtools', 'gtools', 'fastseg', 'rtracklayer', 
                 'mclust', 'R.utils', 'limma', 'Rcpp', 'Rhtslib', 'zlibbioc'))
install.packages('methylkit', repos = "http://www.bioconductor.org/packages/devel/bioc")
ADD REPLYlink written 3.2 years ago by tangming2005150
Answer: load methylKit segfault error
0
gravatar for Martin Morgan
3.2 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

Are your package versions correct? Try BiocInstaller::biocValid() to check.

ADD COMMENTlink written 3.2 years ago by Martin Morgan ♦♦ 24k
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