load methylKit segfault error
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Entering edit mode
tangming2005 ▴ 170
@tangming2005-6754
Last seen 13 months ago
United States

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
methylKit bioconductor • 901 views
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0
Entering edit mode
@altuna-akalin-7813
Last seen 2.7 years ago
Germany/Berlin/MDC-BIMSB

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)
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0
Entering edit mode

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.

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0
Entering edit mode

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")
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0
Entering edit mode
@martin-morgan-1513
Last seen 9 weeks ago
United States

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

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