[Bioc-devel] caught segfault when compiling ensembldb

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Thu Oct 17 16:58:34 CEST 2019

It's hard to tell from the stack trace, but is this reproducible in a new R (devel) session with


? And did you actually install new packages in R-devel, or only re-use packages installed in an earlier version of R? If the latter, then definitely you'll want to re-install ALL packages under R-devel...


On 10/17/19, 10:10 AM, "Bioc-devel on behalf of Zhu, Jack (NIH/NCI) [E] via Bioc-devel" <bioc-devel-bounces using r-project.org on behalf of bioc-devel using r-project.org> wrote:

    Dear all,
    I have encountered a very frustrating 'memory not mapped' problem when compiling ensembldb package:
    >BiocManager::install("ensembldb", ask = FALSE)
    Bioconductor version 3.10 (BiocManager 1.30.8), R Under development (unstable)
      (2019-10-15 r77295)
    Installing package(s) 'ensembldb'
    Warning: unable to access index for repository https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/4.0:
      cannot open URL 'https://bioconductor.org/packages/3.10/bioc/bin/macosx/el-capitan/contrib/4.0/PACKAGES'
    Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/4.0:
      cannot open URL 'https://bioconductor.org/packages/3.10/data/annotation/bin/macosx/el-capitan/contrib/4.0/PACKAGES'
    Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/4.0:
      cannot open URL 'https://bioconductor.org/packages/3.10/data/experiment/bin/macosx/el-capitan/contrib/4.0/PACKAGES'
    Warning: unable to access index for repository https://bioconductor.org/packages/3.10/workflows/bin/macosx/el-capitan/contrib/4.0:
      cannot open URL 'https://bioconductor.org/packages/3.10/workflows/bin/macosx/el-capitan/contrib/4.0/PACKAGES'
    Warning: unable to access index for repository https://cran.rstudio.com/bin/macosx/el-capitan/contrib/4.0:
      cannot open URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/4.0/PACKAGES'
    installing the source package ‘ensembldb’
    trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/ensembldb_2.9.6.tar.gz'
    Content type 'application/x-gzip' length 3313875 bytes (3.2 MB)
    downloaded 3.2 MB
    * installing *source* package ‘ensembldb’ ...
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    sh: line 1: 11388 Segmentation fault: 11  R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-echo 2>&1 < '/var/folders/c0/dsy4zf0d75x8wp0w89r8g89nh1q7rl/T//Rtmp2uO8sw/file2c759026e04'
    *** caught segfault ***
    address 0x2bd90, cause 'memory not mapped'
    1: fun(libname, pkgname)
    2: doTryCatch(return(expr), name, parentenv, handler)
    3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    4: tryCatchList(expr, classes, parentenv, handlers)
    5: tryCatch(fun(libname, pkgname), error = identity)
    6: runHook(".onLoad", env, package.lib, package)
    7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    8: asNamespace(ns)
    9: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
    10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
    11: asNamespace(ns)
    12: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
    13: loadNamespace(package, lib.loc)
    14: doTryCatch(return(expr), name, parentenv, handler)
    15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    16: tryCatchList(expr, classes, parentenv, handlers)
    17: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
    18: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
    19: .getRequiredPackages2(pkgInfo, quietly, lib.loc, useImports)
    20: .getRequiredPackages(quietly = TRUE)
    21: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
    22: suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))
    An irrecoverable exception occurred. R is aborting now ...
    ERROR: lazy loading failed for package ‘ensembldb’
    * removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ensembldb’
    > sessionInfo()
    R Under development (unstable) (2019-10-15 r77295)
    Platform: x86_64-apple-darwin15.6.0 (64-bit)
    Running under: macOS Mojave 10.14.6
    Matrix products: default
    BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.0.dylib
    LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
    [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
    other attached packages:
    [1] BiocManager_1.30.8
    loaded via a namespace (and not attached):
    [1] compiler_4.0.0 tools_4.0.0
    Your insights will be greatly appreciated.
    Yuelin Jack Zhu, MD, MS
    Bioinformatics Specialist
    BG 37 RM 6138
    BETHESDA MD 20814
    Phone:  240-760-7439
    E-mail: zhujack using mail.nih.gov
    	[[alternative HTML version deleted]]
    Bioc-devel using r-project.org mailing list

More information about the Bioc-devel mailing list